Starting phenix.real_space_refine on Mon Oct 13 13:50:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mhw_9120/10_2025/6mhw_9120.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mhw_9120/10_2025/6mhw_9120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mhw_9120/10_2025/6mhw_9120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mhw_9120/10_2025/6mhw_9120.map" model { file = "/net/cci-nas-00/data/ceres_data/6mhw_9120/10_2025/6mhw_9120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mhw_9120/10_2025/6mhw_9120.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 S 92 5.16 5 C 11778 2.51 5 N 2998 2.21 5 O 3032 1.98 5 H 16514 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34414 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 8634 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 13, 'TRANS': 599} Chain breaks: 2 Unresolved non-hydrogen bonds: 508 Unresolved non-hydrogen angles: 615 Unresolved non-hydrogen dihedrals: 414 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ARG:plan': 14, 'GLU:plan': 35, 'GLN:plan1': 4, 'ASP:plan': 17, 'ASN:plan1': 6, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 325 Chain: "B" Number of atoms: 8573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 8573 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 13, 'TRANS': 599} Chain breaks: 2 Unresolved non-hydrogen bonds: 547 Unresolved non-hydrogen angles: 670 Unresolved non-hydrogen dihedrals: 444 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ARG:plan': 15, 'GLU:plan': 37, 'GLN:plan1': 6, 'ASP:plan': 18, 'ASN:plan1': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 5} Unresolved non-hydrogen planarities: 369 Chain: "C" Number of atoms: 8634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 8634 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 13, 'TRANS': 599} Chain breaks: 2 Unresolved non-hydrogen bonds: 508 Unresolved non-hydrogen angles: 615 Unresolved non-hydrogen dihedrals: 414 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ARG:plan': 14, 'GLU:plan': 35, 'GLN:plan1': 4, 'ASP:plan': 17, 'ASN:plan1': 6, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 325 Chain: "D" Number of atoms: 8573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 8573 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 13, 'TRANS': 599} Chain breaks: 2 Unresolved non-hydrogen bonds: 547 Unresolved non-hydrogen angles: 670 Unresolved non-hydrogen dihedrals: 444 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ARG:plan': 15, 'GLU:plan': 37, 'GLN:plan1': 6, 'ASP:plan': 18, 'ASN:plan1': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 5} Unresolved non-hydrogen planarities: 369 Time building chain proxies: 7.09, per 1000 atoms: 0.21 Number of scatterers: 34414 At special positions: 0 Unit cell: (143.75, 139.15, 127.65, 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 92 16.00 O 3032 8.00 N 2998 7.00 C 11778 6.00 H 16514 1.00 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=0, symmetry=0 Time building additional restraints: 3.49 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4688 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 6 sheets defined 68.9% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 114 through 130 Processing helix chain 'A' and resid 132 through 148 removed outlier: 3.716A pdb=" N VAL A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 162 removed outlier: 3.559A pdb=" N PHE A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 178 Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.722A pdb=" N ILE A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 228 through 237 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 369 through 374 removed outlier: 4.358A pdb=" N SER A 372 " --> pdb=" O ARG A 369 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 374 " --> pdb=" O ARG A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 410 removed outlier: 3.902A pdb=" N ASN A 410 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 Processing helix chain 'A' and resid 422 through 436 Processing helix chain 'A' and resid 436 through 461 Processing helix chain 'A' and resid 485 through 508 removed outlier: 4.005A pdb=" N MET A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 497 " --> pdb=" O TRP A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 542 Processing helix chain 'A' and resid 546 through 567 removed outlier: 3.566A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 Processing helix chain 'A' and resid 586 through 609 removed outlier: 3.611A pdb=" N PHE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 Processing helix chain 'A' and resid 650 through 681 removed outlier: 3.946A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL A 681 " --> pdb=" O MET A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 707 removed outlier: 4.393A pdb=" N SER A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'B' and resid 115 through 130 Processing helix chain 'B' and resid 132 through 150 removed outlier: 3.819A pdb=" N VAL B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.557A pdb=" N PHE B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.673A pdb=" N ILE B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 228 through 237 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.721A pdb=" N HIS B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.562A pdb=" N ARG B 371 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER B 372 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 421 Processing helix chain 'B' and resid 422 through 436 Processing helix chain 'B' and resid 436 through 461 Processing helix chain 'B' and resid 485 through 508 removed outlier: 4.485A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 542 removed outlier: 3.590A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 549 Processing helix chain 'B' and resid 550 through 565 removed outlier: 3.589A pdb=" N ALA B 554 " --> pdb=" O CYS B 550 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 569 through 609 removed outlier: 4.056A pdb=" N VAL B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 Processing helix chain 'B' and resid 650 through 680 Processing helix chain 'B' and resid 682 through 707 removed outlier: 3.558A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 716 removed outlier: 3.593A pdb=" N ARG B 712 " --> pdb=" O PRO B 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 130 Processing helix chain 'C' and resid 132 through 148 removed outlier: 3.716A pdb=" N VAL C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 162 removed outlier: 3.556A pdb=" N PHE C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.721A pdb=" N ILE C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 298 through 305 Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 331 through 336 Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 354 through 362 Processing helix chain 'C' and resid 369 through 374 removed outlier: 4.358A pdb=" N SER C 372 " --> pdb=" O ARG C 369 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 374 " --> pdb=" O ARG C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 410 removed outlier: 3.902A pdb=" N ASN C 410 " --> pdb=" O ILE C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 421 Processing helix chain 'C' and resid 422 through 436 Processing helix chain 'C' and resid 436 through 461 Processing helix chain 'C' and resid 485 through 508 removed outlier: 4.004A pdb=" N MET C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N CYS C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE C 497 " --> pdb=" O TRP C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 542 Processing helix chain 'C' and resid 546 through 567 removed outlier: 3.571A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 586 Processing helix chain 'C' and resid 586 through 609 removed outlier: 3.621A pdb=" N PHE C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 Processing helix chain 'C' and resid 650 through 681 removed outlier: 3.948A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL C 681 " --> pdb=" O MET C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 707 removed outlier: 4.393A pdb=" N SER C 685 " --> pdb=" O VAL C 681 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 715 Processing helix chain 'D' and resid 115 through 130 Processing helix chain 'D' and resid 132 through 150 removed outlier: 3.819A pdb=" N VAL D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 163 removed outlier: 3.557A pdb=" N PHE D 157 " --> pdb=" O ASP D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.675A pdb=" N ILE D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 228 through 237 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.721A pdb=" N HIS D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 Processing helix chain 'D' and resid 309 through 314 Processing helix chain 'D' and resid 316 through 328 Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 354 through 362 Processing helix chain 'D' and resid 368 through 374 removed outlier: 3.563A pdb=" N ARG D 371 " --> pdb=" O LYS D 368 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER D 372 " --> pdb=" O ARG D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 421 Processing helix chain 'D' and resid 422 through 436 Processing helix chain 'D' and resid 436 through 461 Processing helix chain 'D' and resid 485 through 508 removed outlier: 4.503A pdb=" N PHE D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 542 removed outlier: 3.588A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU D 541 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 549 Processing helix chain 'D' and resid 550 through 565 removed outlier: 3.585A pdb=" N ALA D 554 " --> pdb=" O CYS D 550 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 568 No H-bonds generated for 'chain 'D' and resid 566 through 568' Processing helix chain 'D' and resid 569 through 609 removed outlier: 4.069A pdb=" N VAL D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE D 583 " --> pdb=" O ILE D 579 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS D 589 " --> pdb=" O HIS D 585 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 Processing helix chain 'D' and resid 650 through 680 Processing helix chain 'D' and resid 682 through 707 removed outlier: 3.560A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 716 removed outlier: 3.594A pdb=" N ARG D 712 " --> pdb=" O PRO D 708 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 163 through 164 Processing sheet with id=AA2, first strand: chain 'A' and resid 377 through 378 Processing sheet with id=AA3, first strand: chain 'B' and resid 377 through 380 removed outlier: 6.933A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 163 through 164 Processing sheet with id=AA5, first strand: chain 'C' and resid 377 through 378 Processing sheet with id=AA6, first strand: chain 'D' and resid 377 through 380 removed outlier: 6.935A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) 1181 hydrogen bonds defined for protein. 3483 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.09 Time building geometry restraints manager: 4.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16482 1.03 - 1.23: 32 1.23 - 1.42: 7666 1.42 - 1.61: 10480 1.61 - 1.81: 148 Bond restraints: 34808 Sorted by residual: bond pdb=" CB VAL D 756 " pdb=" CG2 VAL D 756 " ideal model delta sigma weight residual 1.521 1.559 -0.038 3.30e-02 9.18e+02 1.31e+00 bond pdb=" CB VAL B 756 " pdb=" CG2 VAL B 756 " ideal model delta sigma weight residual 1.521 1.558 -0.037 3.30e-02 9.18e+02 1.29e+00 bond pdb=" CB VAL C 756 " pdb=" CG2 VAL C 756 " ideal model delta sigma weight residual 1.521 1.556 -0.035 3.30e-02 9.18e+02 1.15e+00 bond pdb=" CB VAL A 756 " pdb=" CG2 VAL A 756 " ideal model delta sigma weight residual 1.521 1.556 -0.035 3.30e-02 9.18e+02 1.13e+00 bond pdb=" CG LEU D 608 " pdb=" CD2 LEU D 608 " ideal model delta sigma weight residual 1.521 1.550 -0.029 3.30e-02 9.18e+02 7.80e-01 ... (remaining 34803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.47: 62380 5.47 - 10.93: 30 10.93 - 16.40: 10 16.40 - 21.87: 0 21.87 - 27.33: 48 Bond angle restraints: 62468 Sorted by residual: angle pdb=" CG2 VAL D 756 " pdb=" CB VAL D 756 " pdb=" HB VAL D 756 " ideal model delta sigma weight residual 108.00 80.67 27.33 3.00e+00 1.11e-01 8.30e+01 angle pdb=" CG2 VAL B 756 " pdb=" CB VAL B 756 " pdb=" HB VAL B 756 " ideal model delta sigma weight residual 108.00 80.71 27.29 3.00e+00 1.11e-01 8.28e+01 angle pdb=" CG2 VAL C 756 " pdb=" CB VAL C 756 " pdb=" HB VAL C 756 " ideal model delta sigma weight residual 108.00 81.16 26.84 3.00e+00 1.11e-01 8.01e+01 angle pdb=" CG2 VAL A 756 " pdb=" CB VAL A 756 " pdb=" HB VAL A 756 " ideal model delta sigma weight residual 108.00 81.17 26.83 3.00e+00 1.11e-01 8.00e+01 angle pdb=" CG1 VAL D 756 " pdb=" CB VAL D 756 " pdb=" HB VAL D 756 " ideal model delta sigma weight residual 108.00 81.89 26.11 3.00e+00 1.11e-01 7.58e+01 ... (remaining 62463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.29: 15850 14.29 - 28.59: 661 28.59 - 42.88: 91 42.88 - 57.17: 98 57.17 - 71.46: 22 Dihedral angle restraints: 16722 sinusoidal: 8076 harmonic: 8646 Sorted by residual: dihedral pdb=" CA GLN D 580 " pdb=" C GLN D 580 " pdb=" N LYS D 581 " pdb=" CA LYS D 581 " ideal model delta harmonic sigma weight residual -180.00 -159.96 -20.04 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA GLN B 580 " pdb=" C GLN B 580 " pdb=" N LYS B 581 " pdb=" CA LYS B 581 " ideal model delta harmonic sigma weight residual -180.00 -160.29 -19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA VAL C 681 " pdb=" C VAL C 681 " pdb=" N GLU C 682 " pdb=" CA GLU C 682 " ideal model delta harmonic sigma weight residual -180.00 -163.86 -16.14 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 16719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.370: 3046 0.370 - 0.740: 0 0.740 - 1.110: 0 1.110 - 1.480: 4 1.480 - 1.850: 12 Chirality restraints: 3062 Sorted by residual: chirality pdb=" CG LEU A 541 " pdb=" CB LEU A 541 " pdb=" CD1 LEU A 541 " pdb=" CD2 LEU A 541 " both_signs ideal model delta sigma weight residual False -2.59 -0.74 -1.85 2.00e-01 2.50e+01 8.56e+01 chirality pdb=" CG LEU C 541 " pdb=" CB LEU C 541 " pdb=" CD1 LEU C 541 " pdb=" CD2 LEU C 541 " both_signs ideal model delta sigma weight residual False -2.59 -0.74 -1.85 2.00e-01 2.50e+01 8.55e+01 chirality pdb=" CG LEU A 608 " pdb=" CB LEU A 608 " pdb=" CD1 LEU A 608 " pdb=" CD2 LEU A 608 " both_signs ideal model delta sigma weight residual False -2.59 -0.75 -1.84 2.00e-01 2.50e+01 8.42e+01 ... (remaining 3059 not shown) Planarity restraints: 5474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 550 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.64e+00 pdb=" C CYS A 550 " 0.028 2.00e-02 2.50e+03 pdb=" O CYS A 550 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 551 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 550 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C CYS C 550 " -0.028 2.00e-02 2.50e+03 pdb=" O CYS C 550 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU C 551 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 549 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" C ALA C 549 " -0.025 2.00e-02 2.50e+03 pdb=" O ALA C 549 " 0.009 2.00e-02 2.50e+03 pdb=" N CYS C 550 " 0.008 2.00e-02 2.50e+03 ... (remaining 5471 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 932 2.15 - 2.77: 65058 2.77 - 3.38: 92797 3.38 - 3.99: 114145 3.99 - 4.60: 183532 Nonbonded interactions: 456464 Sorted by model distance: nonbonded pdb=" O LEU A 281 " pdb=" HG1 THR A 287 " model vdw 1.542 2.450 nonbonded pdb=" O LEU C 281 " pdb=" HG1 THR C 287 " model vdw 1.543 2.450 nonbonded pdb=" OD2 ASP C 379 " pdb="HH12 ARG C 733 " model vdw 1.563 2.450 nonbonded pdb=" OD2 ASP A 379 " pdb="HH12 ARG A 733 " model vdw 1.565 2.450 nonbonded pdb=" OE2 GLU B 751 " pdb="HD22 ASN C 178 " model vdw 1.574 2.450 ... (remaining 456459 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.610 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: 0.220 Extract box with map and model: 0.470 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 33.730 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 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 : 0.004 0.038 18294 Z= 0.170 Angle : 0.620 11.739 25002 Z= 0.325 Chirality : 0.129 1.850 3062 Planarity : 0.003 0.034 3086 Dihedral : 7.018 71.464 5912 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.15), residues: 2428 helix: -0.80 (0.11), residues: 1636 sheet: -2.89 (0.48), residues: 68 loop : -2.35 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.020 0.001 TYR A 575 PHE 0.023 0.002 PHE D 597 TRP 0.011 0.001 TRP D 710 HIS 0.006 0.001 HIS B 585 Details of bonding type rmsd covalent geometry : bond 0.00372 (18294) covalent geometry : angle 0.61989 (25002) hydrogen bonds : bond 0.14379 ( 1181) hydrogen bonds : angle 5.72861 ( 3483) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue MET 672 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue MET 672 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 505 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 505 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 579 ILE cc_start: 0.8723 (mt) cc_final: 0.8495 (mt) REVERT: A 691 ILE cc_start: 0.8635 (mt) cc_final: 0.8402 (tp) REVERT: B 297 ASN cc_start: 0.8907 (m-40) cc_final: 0.8509 (m110) REVERT: B 382 TYR cc_start: 0.8309 (t80) cc_final: 0.7805 (t80) REVERT: B 592 PHE cc_start: 0.8312 (t80) cc_final: 0.7883 (t80) REVERT: B 629 VAL cc_start: 0.9375 (t) cc_final: 0.8951 (t) REVERT: B 661 TYR cc_start: 0.8184 (t80) cc_final: 0.7854 (t80) REVERT: C 579 ILE cc_start: 0.8739 (mt) cc_final: 0.8488 (mt) REVERT: D 297 ASN cc_start: 0.8916 (m-40) cc_final: 0.8510 (m110) REVERT: D 382 TYR cc_start: 0.8356 (t80) cc_final: 0.7872 (t80) REVERT: D 592 PHE cc_start: 0.8359 (t80) cc_final: 0.8004 (t80) REVERT: D 629 VAL cc_start: 0.9398 (t) cc_final: 0.8910 (t) REVERT: D 656 PHE cc_start: 0.6957 (t80) cc_final: 0.6712 (t80) REVERT: D 661 TYR cc_start: 0.8164 (t80) cc_final: 0.7942 (t80) outliers start: 0 outliers final: 0 residues processed: 505 average time/residue: 0.3114 time to fit residues: 237.6854 Evaluate side-chains 291 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 301 HIS ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN A 645 GLN A 671 ASN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS ** C 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN C 645 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 HIS ** D 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.101872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.082735 restraints weight = 155766.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.085273 restraints weight = 69158.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.086767 restraints weight = 41226.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.087558 restraints weight = 30286.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.088029 restraints weight = 25700.134| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 18294 Z= 0.220 Angle : 0.688 11.406 25002 Z= 0.352 Chirality : 0.128 1.823 3062 Planarity : 0.004 0.033 3086 Dihedral : 4.301 24.825 2600 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.25 % Allowed : 8.89 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.16), residues: 2428 helix: 0.68 (0.12), residues: 1604 sheet: -2.20 (0.43), residues: 92 loop : -2.30 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 371 TYR 0.015 0.002 TYR A 575 PHE 0.015 0.001 PHE D 157 TRP 0.012 0.001 TRP B 710 HIS 0.008 0.002 HIS D 585 Details of bonding type rmsd covalent geometry : bond 0.00477 (18294) covalent geometry : angle 0.68830 (25002) hydrogen bonds : bond 0.04303 ( 1181) hydrogen bonds : angle 4.58831 ( 3483) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue MET 672 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue MET 672 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 334 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 314 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 691 ILE cc_start: 0.8789 (mt) cc_final: 0.8353 (tp) REVERT: A 695 GLN cc_start: 0.8447 (mt0) cc_final: 0.8217 (mt0) REVERT: B 297 ASN cc_start: 0.9313 (m-40) cc_final: 0.8870 (m110) REVERT: B 592 PHE cc_start: 0.8404 (t80) cc_final: 0.8135 (t80) REVERT: B 661 TYR cc_start: 0.8785 (t80) cc_final: 0.8549 (t80) REVERT: C 695 GLN cc_start: 0.8456 (mt0) cc_final: 0.8239 (mt0) REVERT: D 297 ASN cc_start: 0.9337 (m-40) cc_final: 0.8872 (m110) REVERT: D 431 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7916 (mtp) REVERT: D 532 LEU cc_start: 0.9279 (mt) cc_final: 0.8932 (tt) REVERT: D 592 PHE cc_start: 0.8466 (t80) cc_final: 0.8200 (t80) REVERT: D 661 TYR cc_start: 0.8849 (t80) cc_final: 0.8629 (t80) outliers start: 20 outliers final: 15 residues processed: 327 average time/residue: 0.2632 time to fit residues: 140.5009 Evaluate side-chains 273 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 257 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 561 ASN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 133 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 179 optimal weight: 6.9990 chunk 235 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 394 ASN A 417 HIS A 561 ASN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 ASN C 394 ASN C 417 HIS C 561 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.100032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.080692 restraints weight = 155500.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.083171 restraints weight = 69521.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.084612 restraints weight = 41805.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.085403 restraints weight = 31027.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.085771 restraints weight = 26441.725| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18294 Z= 0.216 Angle : 0.672 11.267 25002 Z= 0.341 Chirality : 0.126 1.774 3062 Planarity : 0.003 0.031 3086 Dihedral : 4.246 21.544 2600 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.75 % Allowed : 9.14 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.16), residues: 2428 helix: 1.35 (0.12), residues: 1580 sheet: -2.01 (0.44), residues: 92 loop : -2.07 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 729 TYR 0.017 0.002 TYR B 321 PHE 0.013 0.001 PHE A 449 TRP 0.011 0.001 TRP A 433 HIS 0.007 0.001 HIS B 430 Details of bonding type rmsd covalent geometry : bond 0.00468 (18294) covalent geometry : angle 0.67189 (25002) hydrogen bonds : bond 0.04068 ( 1181) hydrogen bonds : angle 4.48861 ( 3483) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue MET 672 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue MET 672 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 306 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 278 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 ILE cc_start: 0.8265 (mt) cc_final: 0.7857 (mt) REVERT: A 561 ASN cc_start: 0.9112 (OUTLIER) cc_final: 0.7901 (t0) REVERT: B 297 ASN cc_start: 0.9315 (m-40) cc_final: 0.9042 (m-40) REVERT: B 532 LEU cc_start: 0.9256 (mt) cc_final: 0.8936 (tt) REVERT: B 592 PHE cc_start: 0.8447 (t80) cc_final: 0.8156 (t80) REVERT: B 666 PHE cc_start: 0.8781 (t80) cc_final: 0.8544 (t80) REVERT: C 365 ILE cc_start: 0.8272 (mt) cc_final: 0.7864 (mt) REVERT: C 561 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.7888 (t0) REVERT: D 297 ASN cc_start: 0.9322 (m-40) cc_final: 0.8834 (m110) REVERT: D 431 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7936 (mtp) REVERT: D 532 LEU cc_start: 0.9215 (mt) cc_final: 0.8834 (tt) REVERT: D 592 PHE cc_start: 0.8552 (t80) cc_final: 0.8275 (t80) outliers start: 28 outliers final: 21 residues processed: 299 average time/residue: 0.2264 time to fit residues: 113.3458 Evaluate side-chains 281 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 257 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 561 ASN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 50 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 219 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 197 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 222 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 HIS C 671 ASN D 255 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.099958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.080406 restraints weight = 154936.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.082871 restraints weight = 69057.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.084324 restraints weight = 41691.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.085114 restraints weight = 30913.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.085556 restraints weight = 26372.605| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18294 Z= 0.184 Angle : 0.649 11.201 25002 Z= 0.327 Chirality : 0.125 1.758 3062 Planarity : 0.003 0.030 3086 Dihedral : 4.119 21.161 2600 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.44 % Allowed : 10.45 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.17), residues: 2428 helix: 1.71 (0.13), residues: 1576 sheet: -2.04 (0.43), residues: 92 loop : -2.05 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 416 TYR 0.014 0.002 TYR B 321 PHE 0.018 0.001 PHE A 526 TRP 0.008 0.001 TRP C 380 HIS 0.006 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00402 (18294) covalent geometry : angle 0.64894 (25002) hydrogen bonds : bond 0.03803 ( 1181) hydrogen bonds : angle 4.30281 ( 3483) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue MET 672 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue MET 672 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 295 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 272 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.7625 (t0) REVERT: B 297 ASN cc_start: 0.9305 (m-40) cc_final: 0.8835 (m110) REVERT: B 532 LEU cc_start: 0.9250 (mt) cc_final: 0.8934 (tt) REVERT: B 557 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8758 (tt) REVERT: B 592 PHE cc_start: 0.8465 (t80) cc_final: 0.8151 (t80) REVERT: C 561 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.7581 (t0) REVERT: C 694 LEU cc_start: 0.8982 (tp) cc_final: 0.8719 (tt) REVERT: D 297 ASN cc_start: 0.9293 (m-40) cc_final: 0.8836 (m110) REVERT: D 431 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7933 (mtp) REVERT: D 532 LEU cc_start: 0.9226 (mt) cc_final: 0.8870 (tt) REVERT: D 592 PHE cc_start: 0.8543 (t80) cc_final: 0.8214 (t80) REVERT: D 666 PHE cc_start: 0.8801 (t80) cc_final: 0.8558 (t80) outliers start: 23 outliers final: 13 residues processed: 288 average time/residue: 0.2418 time to fit residues: 115.6027 Evaluate side-chains 271 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 254 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 561 ASN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 523 HIS Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 205 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 172 optimal weight: 0.0980 chunk 174 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 ASN C 561 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.099897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.080303 restraints weight = 154645.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.082787 restraints weight = 69044.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.084243 restraints weight = 41518.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.085048 restraints weight = 30859.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.085453 restraints weight = 26261.043| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18294 Z= 0.166 Angle : 0.639 11.177 25002 Z= 0.317 Chirality : 0.125 1.746 3062 Planarity : 0.003 0.030 3086 Dihedral : 4.003 19.664 2600 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.44 % Allowed : 10.58 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.17), residues: 2428 helix: 1.92 (0.13), residues: 1576 sheet: -2.10 (0.43), residues: 92 loop : -2.04 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 696 TYR 0.015 0.001 TYR B 321 PHE 0.014 0.001 PHE C 526 TRP 0.010 0.001 TRP C 692 HIS 0.006 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00363 (18294) covalent geometry : angle 0.63916 (25002) hydrogen bonds : bond 0.03633 ( 1181) hydrogen bonds : angle 4.17564 ( 3483) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue MET 672 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue MET 672 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 299 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 276 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 ASN cc_start: 0.9170 (OUTLIER) cc_final: 0.7848 (t0) REVERT: A 633 PHE cc_start: 0.8750 (m-80) cc_final: 0.8364 (t80) REVERT: B 297 ASN cc_start: 0.9297 (m-40) cc_final: 0.8833 (m110) REVERT: B 592 PHE cc_start: 0.8456 (t80) cc_final: 0.8095 (t80) REVERT: B 666 PHE cc_start: 0.8829 (t80) cc_final: 0.8573 (t80) REVERT: C 561 ASN cc_start: 0.9159 (OUTLIER) cc_final: 0.7907 (t0) REVERT: D 297 ASN cc_start: 0.9305 (m-40) cc_final: 0.8862 (m110) REVERT: D 431 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7996 (mtp) REVERT: D 532 LEU cc_start: 0.9220 (mt) cc_final: 0.8866 (tt) REVERT: D 592 PHE cc_start: 0.8463 (t80) cc_final: 0.8144 (t80) REVERT: D 666 PHE cc_start: 0.8823 (t80) cc_final: 0.8579 (t80) outliers start: 23 outliers final: 15 residues processed: 294 average time/residue: 0.2445 time to fit residues: 120.1805 Evaluate side-chains 277 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 259 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 ASN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 523 HIS Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 33 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 186 optimal weight: 10.0000 chunk 198 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.099108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.079500 restraints weight = 154210.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.081950 restraints weight = 69012.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.083400 restraints weight = 41609.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.084170 restraints weight = 30905.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.084591 restraints weight = 26454.741| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18294 Z= 0.187 Angle : 0.649 11.179 25002 Z= 0.324 Chirality : 0.124 1.740 3062 Planarity : 0.003 0.029 3086 Dihedral : 4.013 19.515 2600 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.31 % Allowed : 11.45 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.17), residues: 2428 helix: 1.93 (0.13), residues: 1580 sheet: -2.24 (0.42), residues: 92 loop : -2.04 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 729 TYR 0.014 0.002 TYR D 650 PHE 0.017 0.001 PHE C 526 TRP 0.013 0.001 TRP A 692 HIS 0.006 0.001 HIS B 430 Details of bonding type rmsd covalent geometry : bond 0.00407 (18294) covalent geometry : angle 0.64896 (25002) hydrogen bonds : bond 0.03632 ( 1181) hydrogen bonds : angle 4.20740 ( 3483) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue MET 672 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue MET 672 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 284 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 263 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 ASN cc_start: 0.9099 (OUTLIER) cc_final: 0.8362 (t0) REVERT: A 694 LEU cc_start: 0.8953 (tp) cc_final: 0.8693 (tt) REVERT: B 666 PHE cc_start: 0.8823 (t80) cc_final: 0.8593 (t80) REVERT: D 431 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.8000 (mtp) REVERT: D 532 LEU cc_start: 0.9218 (mt) cc_final: 0.8869 (tt) REVERT: D 666 PHE cc_start: 0.8642 (t80) cc_final: 0.8349 (t80) outliers start: 21 outliers final: 19 residues processed: 280 average time/residue: 0.2489 time to fit residues: 117.0625 Evaluate side-chains 265 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 244 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 561 ASN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 116 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 98 optimal weight: 0.0770 chunk 193 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 206 optimal weight: 1.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.099245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.079514 restraints weight = 153775.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.082008 restraints weight = 68789.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.083471 restraints weight = 41441.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.084256 restraints weight = 30775.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.084675 restraints weight = 26161.509| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18294 Z= 0.160 Angle : 0.633 11.148 25002 Z= 0.312 Chirality : 0.124 1.734 3062 Planarity : 0.003 0.033 3086 Dihedral : 3.927 19.649 2600 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.38 % Allowed : 12.14 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.17), residues: 2428 helix: 2.03 (0.13), residues: 1608 sheet: -2.21 (0.43), residues: 92 loop : -2.04 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 729 TYR 0.013 0.001 TYR B 321 PHE 0.015 0.001 PHE C 526 TRP 0.012 0.001 TRP C 692 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00351 (18294) covalent geometry : angle 0.63254 (25002) hydrogen bonds : bond 0.03475 ( 1181) hydrogen bonds : angle 4.06606 ( 3483) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue MET 672 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue MET 672 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 291 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 269 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 ASN cc_start: 0.9272 (OUTLIER) cc_final: 0.8195 (t0) REVERT: B 532 LEU cc_start: 0.9210 (mt) cc_final: 0.8891 (tt) REVERT: B 666 PHE cc_start: 0.8805 (t80) cc_final: 0.8572 (t80) REVERT: C 561 ASN cc_start: 0.9268 (OUTLIER) cc_final: 0.8137 (t0) REVERT: D 431 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.8031 (mtp) REVERT: D 532 LEU cc_start: 0.9210 (mt) cc_final: 0.8854 (tt) REVERT: D 666 PHE cc_start: 0.8639 (t80) cc_final: 0.8364 (t80) outliers start: 22 outliers final: 18 residues processed: 287 average time/residue: 0.2495 time to fit residues: 119.2710 Evaluate side-chains 274 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 253 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 561 ASN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 35 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 HIS C 297 ASN ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.098262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.078560 restraints weight = 154317.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.080982 restraints weight = 69522.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.082420 restraints weight = 41884.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.083215 restraints weight = 31126.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.083634 restraints weight = 26453.589| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18294 Z= 0.196 Angle : 0.657 11.183 25002 Z= 0.328 Chirality : 0.125 1.755 3062 Planarity : 0.003 0.028 3086 Dihedral : 4.012 19.231 2600 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.69 % Allowed : 12.20 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.17), residues: 2428 helix: 1.94 (0.12), residues: 1608 sheet: -2.80 (0.46), residues: 68 loop : -2.01 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 729 TYR 0.014 0.002 TYR A 650 PHE 0.015 0.001 PHE C 526 TRP 0.014 0.001 TRP A 692 HIS 0.006 0.001 HIS B 430 Details of bonding type rmsd covalent geometry : bond 0.00426 (18294) covalent geometry : angle 0.65699 (25002) hydrogen bonds : bond 0.03597 ( 1181) hydrogen bonds : angle 4.16984 ( 3483) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue MET 672 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue MET 672 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 286 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 259 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 ASN cc_start: 0.9274 (OUTLIER) cc_final: 0.8170 (t0) REVERT: B 532 LEU cc_start: 0.9213 (mt) cc_final: 0.8887 (tt) REVERT: B 666 PHE cc_start: 0.8842 (t80) cc_final: 0.8600 (t80) REVERT: C 561 ASN cc_start: 0.9244 (OUTLIER) cc_final: 0.8455 (t0) REVERT: D 431 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8076 (mtp) REVERT: D 532 LEU cc_start: 0.9201 (mt) cc_final: 0.8824 (tt) REVERT: D 666 PHE cc_start: 0.8650 (t80) cc_final: 0.8349 (t80) outliers start: 27 outliers final: 20 residues processed: 280 average time/residue: 0.2406 time to fit residues: 114.4169 Evaluate side-chains 272 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 249 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 561 ASN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 117 optimal weight: 0.6980 chunk 183 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 190 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.098941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.079268 restraints weight = 152797.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.081776 restraints weight = 67805.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.083230 restraints weight = 40563.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.084012 restraints weight = 29972.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.084327 restraints weight = 25423.849| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18294 Z= 0.155 Angle : 0.636 11.150 25002 Z= 0.313 Chirality : 0.124 1.742 3062 Planarity : 0.003 0.033 3086 Dihedral : 3.901 19.411 2600 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.69 % Allowed : 12.33 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.17), residues: 2428 helix: 2.17 (0.13), residues: 1584 sheet: -2.79 (0.45), residues: 68 loop : -1.91 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 363 TYR 0.013 0.001 TYR B 321 PHE 0.013 0.001 PHE C 526 TRP 0.012 0.001 TRP A 692 HIS 0.004 0.001 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00342 (18294) covalent geometry : angle 0.63638 (25002) hydrogen bonds : bond 0.03436 ( 1181) hydrogen bonds : angle 4.01184 ( 3483) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue MET 672 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue MET 672 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 296 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 269 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 ASN cc_start: 0.9312 (OUTLIER) cc_final: 0.8731 (t0) REVERT: B 532 LEU cc_start: 0.9192 (mt) cc_final: 0.8854 (tt) REVERT: B 666 PHE cc_start: 0.8743 (t80) cc_final: 0.8474 (t80) REVERT: C 561 ASN cc_start: 0.9316 (OUTLIER) cc_final: 0.8747 (t0) REVERT: D 431 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.8067 (mtp) REVERT: D 532 LEU cc_start: 0.9178 (mt) cc_final: 0.8800 (tt) REVERT: D 666 PHE cc_start: 0.8623 (t80) cc_final: 0.8334 (t80) outliers start: 27 outliers final: 21 residues processed: 290 average time/residue: 0.2491 time to fit residues: 120.1189 Evaluate side-chains 279 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 255 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 561 ASN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 185 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.098459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.078724 restraints weight = 153999.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.081194 restraints weight = 69022.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.082649 restraints weight = 41642.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.083441 restraints weight = 30905.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.083861 restraints weight = 26288.986| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.5613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18294 Z= 0.176 Angle : 0.653 11.174 25002 Z= 0.323 Chirality : 0.124 1.727 3062 Planarity : 0.003 0.061 3086 Dihedral : 3.911 18.747 2600 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.50 % Allowed : 13.08 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.17), residues: 2428 helix: 2.07 (0.12), residues: 1588 sheet: -2.88 (0.45), residues: 68 loop : -1.93 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 416 TYR 0.013 0.002 TYR A 650 PHE 0.014 0.001 PHE C 526 TRP 0.014 0.001 TRP A 692 HIS 0.005 0.001 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00385 (18294) covalent geometry : angle 0.65274 (25002) hydrogen bonds : bond 0.03495 ( 1181) hydrogen bonds : angle 4.07543 ( 3483) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue MET 672 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue MET 572 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue MET 672 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 115 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue VAL 499 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue TYR 547 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 286 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 262 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 ASN cc_start: 0.9310 (OUTLIER) cc_final: 0.8724 (t0) REVERT: B 532 LEU cc_start: 0.9195 (mt) cc_final: 0.8857 (tt) REVERT: B 666 PHE cc_start: 0.8779 (t80) cc_final: 0.8497 (t80) REVERT: C 561 ASN cc_start: 0.9315 (OUTLIER) cc_final: 0.8743 (t0) REVERT: D 431 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.8096 (mtp) REVERT: D 532 LEU cc_start: 0.9179 (mt) cc_final: 0.8812 (tt) REVERT: D 666 PHE cc_start: 0.8634 (t80) cc_final: 0.8365 (t80) outliers start: 24 outliers final: 20 residues processed: 281 average time/residue: 0.2395 time to fit residues: 114.0287 Evaluate side-chains 274 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 251 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 561 ASN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 561 ASN Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 536 SER Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 0.9990 chunk 222 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 230 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 186 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.099120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.079354 restraints weight = 153126.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.081853 restraints weight = 68599.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.083306 restraints weight = 41254.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.084094 restraints weight = 30595.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.084519 restraints weight = 26102.427| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18294 Z= 0.147 Angle : 0.633 11.175 25002 Z= 0.310 Chirality : 0.124 1.725 3062 Planarity : 0.003 0.046 3086 Dihedral : 3.825 18.855 2600 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.50 % Allowed : 13.14 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.17), residues: 2428 helix: 2.26 (0.13), residues: 1584 sheet: -2.84 (0.45), residues: 68 loop : -1.92 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 416 TYR 0.013 0.001 TYR B 321 PHE 0.013 0.001 PHE A 526 TRP 0.013 0.001 TRP A 692 HIS 0.004 0.001 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00326 (18294) covalent geometry : angle 0.63327 (25002) hydrogen bonds : bond 0.03388 ( 1181) hydrogen bonds : angle 3.93890 ( 3483) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5312.56 seconds wall clock time: 91 minutes 34.67 seconds (5494.67 seconds total)