Starting phenix.real_space_refine on Thu Nov 20 08:21:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mho_9115/11_2025/6mho_9115.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mho_9115/11_2025/6mho_9115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mho_9115/11_2025/6mho_9115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mho_9115/11_2025/6mho_9115.map" model { file = "/net/cci-nas-00/data/ceres_data/6mho_9115/11_2025/6mho_9115.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mho_9115/11_2025/6mho_9115.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 76 5.16 5 C 11252 2.51 5 N 2844 2.21 5 O 2868 1.98 5 H 15184 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32224 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 8056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 8056 Classifications: {'peptide': 601} Link IDs: {'PTRANS': 12, 'TRANS': 588} Chain breaks: 4 Unresolved non-hydrogen bonds: 644 Unresolved non-hydrogen angles: 793 Unresolved non-hydrogen dihedrals: 522 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ARG:plan': 16, 'GLU:plan': 41, 'GLN:plan1': 7, 'ASN:plan1': 9, 'ASP:plan': 17, 'TYR:plan': 2, 'HIS:plan': 3, 'TRP:plan': 1, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 403 Restraints were copied for chains: C, A, D Time building chain proxies: 10.28, per 1000 atoms: 0.32 Number of scatterers: 32224 At special positions: 0 Unit cell: (127.07, 127.07, 120.52, 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 76 16.00 O 2868 8.00 N 2844 7.00 C 11252 6.00 H 15184 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: 3.18 Conformation dependent library (CDL) restraints added in 1.1 seconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4584 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 8 sheets defined 68.3% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'B' and resid 118 through 130 removed outlier: 4.019A pdb=" N ARG B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 147 removed outlier: 3.860A pdb=" N VAL B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 removed outlier: 3.598A pdb=" N HIS B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 178 removed outlier: 3.591A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.662A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.625A pdb=" N ASN B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 227 through 237 removed outlier: 3.599A pdb=" N ALA B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.676A pdb=" N HIS B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 307 removed outlier: 3.541A pdb=" N ALA B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 315 through 328 removed outlier: 3.947A pdb=" N ARG B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) 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 361 removed outlier: 3.755A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 402 through 410 removed outlier: 3.725A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.881A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 removed outlier: 3.800A pdb=" N TYR B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 506 removed outlier: 3.959A pdb=" N LEU B 485 " --> pdb=" O TRP B 481 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 542 removed outlier: 4.014A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE B 528 " --> pdb=" O PHE B 524 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 562 removed outlier: 4.050A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 568 Processing helix chain 'B' and resid 570 through 609 removed outlier: 4.547A pdb=" N MET B 574 " --> pdb=" O GLN B 570 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL B 587 " --> pdb=" O ILE B 583 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'B' and resid 624 through 638 removed outlier: 3.834A pdb=" N ILE B 637 " --> pdb=" O PHE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 681 removed outlier: 4.286A pdb=" N VAL B 681 " --> pdb=" O MET B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 705 removed outlier: 3.513A pdb=" N LYS B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 716 removed outlier: 3.585A pdb=" N SER B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 130 Processing helix chain 'C' and resid 132 through 147 removed outlier: 3.860A pdb=" N VAL C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 162 removed outlier: 3.598A pdb=" N HIS C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 178 removed outlier: 3.591A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.663A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.625A pdb=" N ASN C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 227 through 237 removed outlier: 3.599A pdb=" N ALA C 231 " --> pdb=" O GLN C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.676A pdb=" N HIS C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 307 removed outlier: 3.541A pdb=" N ALA C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'C' and resid 315 through 328 removed outlier: 3.947A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 325 " --> pdb=" O TYR C 321 " (cutoff:3.500A) 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 361 removed outlier: 3.756A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 402 through 410 removed outlier: 3.725A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.881A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 removed outlier: 3.800A pdb=" N TYR C 461 " --> pdb=" O LEU C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 506 removed outlier: 3.960A pdb=" N LEU C 485 " --> pdb=" O TRP C 481 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 542 removed outlier: 4.014A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE C 528 " --> pdb=" O PHE C 524 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 541 " --> pdb=" O VAL C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 562 removed outlier: 4.050A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 568 Processing helix chain 'C' and resid 570 through 609 removed outlier: 4.546A pdb=" N MET C 574 " --> pdb=" O GLN C 570 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL C 587 " --> pdb=" O ILE C 583 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 612 No H-bonds generated for 'chain 'C' and resid 610 through 612' Processing helix chain 'C' and resid 624 through 638 removed outlier: 3.834A pdb=" N ILE C 637 " --> pdb=" O PHE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 681 removed outlier: 4.285A pdb=" N VAL C 681 " --> pdb=" O MET C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 705 removed outlier: 3.514A pdb=" N LYS C 705 " --> pdb=" O LEU C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 716 removed outlier: 3.584A pdb=" N SER C 713 " --> pdb=" O GLU C 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 130 Processing helix chain 'A' and resid 132 through 147 removed outlier: 3.860A pdb=" N VAL A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 removed outlier: 3.598A pdb=" N HIS A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 178 removed outlier: 3.591A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.662A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.625A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.598A pdb=" N ALA A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.676A pdb=" N HIS A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.541A pdb=" N ALA A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 315 through 328 removed outlier: 3.947A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) 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 361 removed outlier: 3.756A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 402 through 410 removed outlier: 3.724A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.882A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 removed outlier: 3.800A pdb=" N TYR A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 506 removed outlier: 3.959A pdb=" N LEU A 485 " --> pdb=" O TRP A 481 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 542 removed outlier: 4.013A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 528 " --> pdb=" O PHE A 524 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 562 removed outlier: 4.050A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 568 Processing helix chain 'A' and resid 570 through 609 removed outlier: 4.547A pdb=" N MET A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL A 587 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 624 through 638 removed outlier: 3.834A pdb=" N ILE A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 681 removed outlier: 4.286A pdb=" N VAL A 681 " --> pdb=" O MET A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 705 removed outlier: 3.514A pdb=" N LYS A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 716 removed outlier: 3.585A pdb=" N SER A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 Processing helix chain 'D' and resid 132 through 147 removed outlier: 3.861A pdb=" N VAL D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 162 removed outlier: 3.598A pdb=" N HIS D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 178 removed outlier: 3.592A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.662A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.625A pdb=" N ASN D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 227 through 237 removed outlier: 3.599A pdb=" N ALA D 231 " --> pdb=" O GLN D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.676A pdb=" N HIS D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 307 removed outlier: 3.541A pdb=" N ALA D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 314 Processing helix chain 'D' and resid 315 through 328 removed outlier: 3.947A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) 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 361 removed outlier: 3.756A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 402 through 410 removed outlier: 3.724A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.882A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 removed outlier: 3.799A pdb=" N TYR D 461 " --> pdb=" O LEU D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 506 removed outlier: 3.959A pdb=" N LEU D 485 " --> pdb=" O TRP D 481 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 542 removed outlier: 4.014A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE D 528 " --> pdb=" O PHE D 524 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU D 541 " --> pdb=" O VAL D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 562 removed outlier: 4.050A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 568 Processing helix chain 'D' and resid 570 through 609 removed outlier: 4.547A pdb=" N MET D 574 " --> pdb=" O GLN D 570 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL D 587 " --> pdb=" O ILE D 583 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS D 589 " --> pdb=" O HIS D 585 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE D 590 " --> pdb=" O ASP D 586 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE D 597 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 612 No H-bonds generated for 'chain 'D' and resid 610 through 612' Processing helix chain 'D' and resid 624 through 638 removed outlier: 3.834A pdb=" N ILE D 637 " --> pdb=" O PHE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 681 removed outlier: 4.287A pdb=" N VAL D 681 " --> pdb=" O MET D 677 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 705 removed outlier: 3.514A pdb=" N LYS D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 716 removed outlier: 3.585A pdb=" N SER D 713 " --> pdb=" O GLU D 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 163 through 164 Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 378 removed outlier: 4.005A pdb=" N ARG B 729 " --> pdb=" O CYS B 721 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS B 721 " --> pdb=" O ARG B 729 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 163 through 164 Processing sheet with id=AA4, first strand: chain 'C' and resid 376 through 378 removed outlier: 4.005A pdb=" N ARG C 729 " --> pdb=" O CYS C 721 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS C 721 " --> pdb=" O ARG C 729 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 164 Processing sheet with id=AA6, first strand: chain 'A' and resid 376 through 378 removed outlier: 4.006A pdb=" N ARG A 729 " --> pdb=" O CYS A 721 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS A 721 " --> pdb=" O ARG A 729 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 163 through 164 Processing sheet with id=AA8, first strand: chain 'D' and resid 376 through 378 removed outlier: 4.006A pdb=" N ARG D 729 " --> pdb=" O CYS D 721 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS D 721 " --> pdb=" O ARG D 729 " (cutoff:3.500A) 1076 hydrogen bonds defined for protein. 3144 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: 7.11 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 15164 1.02 - 1.22: 20 1.22 - 1.41: 7274 1.41 - 1.61: 10010 1.61 - 1.81: 128 Bond restraints: 32596 Sorted by residual: bond pdb=" NE ARG B 696 " pdb=" HE ARG B 696 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" NE ARG D 696 " pdb=" HE ARG D 696 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" NE ARG A 696 " pdb=" HE ARG A 696 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" NE ARG C 696 " pdb=" HE ARG C 696 " ideal model delta sigma weight residual 0.860 0.969 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" CZ ARG C 567 " pdb=" NH2 ARG C 567 " ideal model delta sigma weight residual 1.330 1.310 0.020 1.30e-02 5.92e+03 2.30e+00 ... (remaining 32591 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 54527 1.50 - 3.00: 3528 3.00 - 4.51: 213 4.51 - 6.01: 68 6.01 - 7.51: 4 Bond angle restraints: 58340 Sorted by residual: angle pdb=" CA TRP D 380 " pdb=" CB TRP D 380 " pdb=" CG TRP D 380 " ideal model delta sigma weight residual 113.60 119.01 -5.41 1.90e+00 2.77e-01 8.10e+00 angle pdb=" CA TRP C 380 " pdb=" CB TRP C 380 " pdb=" CG TRP C 380 " ideal model delta sigma weight residual 113.60 119.01 -5.41 1.90e+00 2.77e-01 8.10e+00 angle pdb=" CA TRP B 380 " pdb=" CB TRP B 380 " pdb=" CG TRP B 380 " ideal model delta sigma weight residual 113.60 119.00 -5.40 1.90e+00 2.77e-01 8.07e+00 angle pdb=" CA TRP A 380 " pdb=" CB TRP A 380 " pdb=" CG TRP A 380 " ideal model delta sigma weight residual 113.60 118.97 -5.37 1.90e+00 2.77e-01 8.00e+00 angle pdb=" N GLU D 725 " pdb=" CA GLU D 725 " pdb=" C GLU D 725 " ideal model delta sigma weight residual 111.07 108.14 2.93 1.07e+00 8.73e-01 7.48e+00 ... (remaining 58335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.41: 14995 13.41 - 26.82: 597 26.82 - 40.23: 71 40.23 - 53.64: 93 53.64 - 67.05: 44 Dihedral angle restraints: 15800 sinusoidal: 7344 harmonic: 8456 Sorted by residual: dihedral pdb=" CA THR D 680 " pdb=" C THR D 680 " pdb=" N VAL D 681 " pdb=" CA VAL D 681 " ideal model delta harmonic sigma weight residual -180.00 -154.87 -25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA THR B 680 " pdb=" C THR B 680 " pdb=" N VAL B 681 " pdb=" CA VAL B 681 " ideal model delta harmonic sigma weight residual 180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA THR C 680 " pdb=" C THR C 680 " pdb=" N VAL C 681 " pdb=" CA VAL C 681 " ideal model delta harmonic sigma weight residual -180.00 -154.91 -25.09 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 15797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1935 0.035 - 0.070: 710 0.070 - 0.104: 235 0.104 - 0.139: 68 0.139 - 0.174: 4 Chirality restraints: 2952 Sorted by residual: chirality pdb=" CB THR D 305 " pdb=" CA THR D 305 " pdb=" OG1 THR D 305 " pdb=" CG2 THR D 305 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" CB THR C 305 " pdb=" CA THR C 305 " pdb=" OG1 THR C 305 " pdb=" CG2 THR C 305 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CB THR B 305 " pdb=" CA THR B 305 " pdb=" OG1 THR B 305 " pdb=" CG2 THR B 305 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.27e-01 ... (remaining 2949 not shown) Planarity restraints: 5280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 449 " 0.020 2.00e-02 2.50e+03 1.19e-02 4.24e+00 pdb=" CG PHE C 449 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE C 449 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 449 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 449 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 449 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 449 " 0.015 2.00e-02 2.50e+03 pdb=" HD1 PHE C 449 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE C 449 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE C 449 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE C 449 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE C 449 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 449 " 0.020 2.00e-02 2.50e+03 1.18e-02 4.20e+00 pdb=" CG PHE A 449 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 449 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 449 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 449 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 449 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 449 " 0.015 2.00e-02 2.50e+03 pdb=" HD1 PHE A 449 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE A 449 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE A 449 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 449 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 449 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 449 " 0.020 2.00e-02 2.50e+03 1.18e-02 4.17e+00 pdb=" CG PHE D 449 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE D 449 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE D 449 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 449 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE D 449 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 449 " 0.015 2.00e-02 2.50e+03 pdb=" HD1 PHE D 449 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE D 449 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE D 449 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE D 449 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE D 449 " -0.002 2.00e-02 2.50e+03 ... (remaining 5277 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 2450 2.26 - 2.85: 69377 2.85 - 3.43: 79856 3.43 - 4.02: 106081 4.02 - 4.60: 163958 Nonbonded interactions: 421722 Sorted by model distance: nonbonded pdb=" O LEU B 281 " pdb=" HG1 THR B 287 " model vdw 1.681 2.450 nonbonded pdb=" O LEU A 281 " pdb=" HG1 THR A 287 " model vdw 1.681 2.450 nonbonded pdb=" O LEU C 281 " pdb=" HG1 THR C 287 " model vdw 1.681 2.450 nonbonded pdb=" O LEU D 281 " pdb=" HG1 THR D 287 " model vdw 1.682 2.450 nonbonded pdb=" O VAL C 723 " pdb=" H ASP C 727 " model vdw 1.699 2.450 ... (remaining 421717 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: 0.06 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'A' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.240 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 34.990 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 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 : 0.005 0.053 17412 Z= 0.218 Angle : 0.719 7.508 23844 Z= 0.390 Chirality : 0.042 0.174 2952 Planarity : 0.004 0.031 2944 Dihedral : 7.356 67.054 5396 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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 are not related in a simple way. whole: -2.41 (0.15), residues: 2364 helix: -1.45 (0.11), residues: 1492 sheet: -1.52 (0.54), residues: 64 loop : -1.55 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 567 TYR 0.014 0.002 TYR D 321 PHE 0.031 0.003 PHE C 449 TRP 0.014 0.002 TRP C 433 HIS 0.008 0.002 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00496 (17412) covalent geometry : angle 0.71855 (23844) hydrogen bonds : bond 0.13982 ( 1076) hydrogen bonds : angle 5.49759 ( 3144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Evaluate side-chains 530 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 530 time to evaluate : 0.839 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: B 599 LEU cc_start: 0.8300 (mt) cc_final: 0.8096 (mt) REVERT: B 636 THR cc_start: 0.9083 (t) cc_final: 0.8860 (m) REVERT: C 156 ASP cc_start: 0.7925 (m-30) cc_final: 0.7705 (t0) REVERT: C 446 CYS cc_start: 0.7436 (m) cc_final: 0.6890 (m) REVERT: C 496 CYS cc_start: 0.7873 (m) cc_final: 0.7653 (m) REVERT: C 603 VAL cc_start: 0.8446 (m) cc_final: 0.8201 (p) REVERT: C 630 LEU cc_start: 0.8748 (tp) cc_final: 0.8205 (mt) REVERT: A 446 CYS cc_start: 0.7587 (m) cc_final: 0.7011 (m) REVERT: A 496 CYS cc_start: 0.7847 (m) cc_final: 0.7632 (m) REVERT: A 630 LEU cc_start: 0.8924 (tp) cc_final: 0.8317 (mt) REVERT: D 626 SER cc_start: 0.7902 (t) cc_final: 0.7392 (p) REVERT: D 630 LEU cc_start: 0.8520 (tp) cc_final: 0.8106 (mt) outliers start: 0 outliers final: 0 residues processed: 530 average time/residue: 0.3095 time to fit residues: 240.8034 Evaluate side-chains 310 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 HIS B 346 GLN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS C 346 GLN C 671 ASN A 301 HIS A 346 GLN A 671 ASN D 301 HIS D 671 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.129208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.105745 restraints weight = 86224.446| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.30 r_work: 0.3186 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 17412 Z= 0.276 Angle : 0.627 6.058 23844 Z= 0.351 Chirality : 0.038 0.134 2952 Planarity : 0.004 0.056 2944 Dihedral : 4.749 20.363 2528 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.93 % Allowed : 9.14 % Favored : 88.93 % 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 are not related in a simple way. whole: -1.18 (0.16), residues: 2364 helix: -0.22 (0.12), residues: 1528 sheet: -2.47 (0.46), residues: 64 loop : -1.58 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 567 TYR 0.025 0.003 TYR D 564 PHE 0.022 0.002 PHE D 310 TRP 0.017 0.002 TRP B 559 HIS 0.006 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00614 (17412) covalent geometry : angle 0.62651 (23844) hydrogen bonds : bond 0.04257 ( 1076) hydrogen bonds : angle 4.35751 ( 3144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Evaluate side-chains 335 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 308 time to evaluate : 0.921 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: B 155 PRO cc_start: 0.7732 (Cg_exo) cc_final: 0.7490 (Cg_endo) REVERT: B 636 THR cc_start: 0.9166 (t) cc_final: 0.8795 (m) REVERT: C 166 ASP cc_start: 0.6455 (t0) cc_final: 0.6211 (t0) REVERT: C 496 CYS cc_start: 0.8542 (m) cc_final: 0.8305 (m) REVERT: A 496 CYS cc_start: 0.8500 (m) cc_final: 0.8256 (m) REVERT: A 630 LEU cc_start: 0.9078 (tp) cc_final: 0.8464 (mt) REVERT: A 671 ASN cc_start: 0.8139 (t160) cc_final: 0.7829 (t0) REVERT: D 630 LEU cc_start: 0.8933 (tp) cc_final: 0.8244 (mt) outliers start: 27 outliers final: 15 residues processed: 325 average time/residue: 0.2423 time to fit residues: 125.8476 Evaluate side-chains 278 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 263 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 701 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 93 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 202 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 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 = 0.3631 r_free = 0.3631 target = 0.130127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.106723 restraints weight = 85895.095| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.30 r_work: 0.3203 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17412 Z= 0.141 Angle : 0.486 4.794 23844 Z= 0.267 Chirality : 0.034 0.127 2952 Planarity : 0.003 0.034 2944 Dihedral : 4.103 19.280 2528 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.79 % Allowed : 10.71 % Favored : 87.50 % 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 are not related in a simple way. whole: -0.22 (0.17), residues: 2364 helix: 0.69 (0.13), residues: 1552 sheet: -2.02 (0.50), residues: 68 loop : -1.66 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 696 TYR 0.016 0.002 TYR D 564 PHE 0.013 0.001 PHE C 193 TRP 0.014 0.001 TRP A 380 HIS 0.003 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00311 (17412) covalent geometry : angle 0.48625 (23844) hydrogen bonds : bond 0.03468 ( 1076) hydrogen bonds : angle 3.83976 ( 3144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Evaluate side-chains 321 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 296 time to evaluate : 0.826 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: B 155 PRO cc_start: 0.7635 (Cg_exo) cc_final: 0.7399 (Cg_endo) REVERT: B 166 ASP cc_start: 0.6657 (t0) cc_final: 0.6428 (t0) REVERT: B 636 THR cc_start: 0.9115 (t) cc_final: 0.8750 (m) REVERT: B 655 LEU cc_start: 0.9258 (tp) cc_final: 0.9056 (tp) REVERT: C 496 CYS cc_start: 0.8507 (m) cc_final: 0.8274 (m) REVERT: A 496 CYS cc_start: 0.8496 (m) cc_final: 0.8278 (m) REVERT: A 599 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8309 (mp) REVERT: A 630 LEU cc_start: 0.9057 (tp) cc_final: 0.8483 (mt) REVERT: D 166 ASP cc_start: 0.6650 (t0) cc_final: 0.6437 (t0) REVERT: D 555 MET cc_start: 0.8262 (tmm) cc_final: 0.8009 (tmm) REVERT: D 563 LEU cc_start: 0.9150 (tt) cc_final: 0.8777 (mp) REVERT: D 630 LEU cc_start: 0.9012 (tp) cc_final: 0.8366 (mt) outliers start: 25 outliers final: 18 residues processed: 312 average time/residue: 0.2310 time to fit residues: 118.3215 Evaluate side-chains 287 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 268 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 583 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 150 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 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 = 0.3542 r_free = 0.3542 target = 0.123523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.100734 restraints weight = 87614.477| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.17 r_work: 0.3109 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 17412 Z= 0.281 Angle : 0.616 5.965 23844 Z= 0.345 Chirality : 0.038 0.137 2952 Planarity : 0.004 0.051 2944 Dihedral : 4.564 18.961 2528 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.86 % Allowed : 10.86 % Favored : 86.29 % 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 are not related in a simple way. whole: -0.62 (0.16), residues: 2364 helix: 0.47 (0.13), residues: 1564 sheet: -2.20 (0.54), residues: 68 loop : -2.11 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 225 TYR 0.019 0.002 TYR D 564 PHE 0.022 0.002 PHE C 316 TRP 0.024 0.002 TRP D 380 HIS 0.006 0.002 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00640 (17412) covalent geometry : angle 0.61566 (23844) hydrogen bonds : bond 0.04088 ( 1076) hydrogen bonds : angle 4.27809 ( 3144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Evaluate side-chains 309 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 269 time to evaluate : 0.758 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: B 155 PRO cc_start: 0.7756 (Cg_exo) cc_final: 0.7499 (Cg_endo) REVERT: A 599 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8454 (mp) REVERT: A 676 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8193 (mp) REVERT: D 166 ASP cc_start: 0.6752 (t0) cc_final: 0.6523 (t0) REVERT: D 419 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8092 (mtt) REVERT: D 489 PHE cc_start: 0.7091 (t80) cc_final: 0.6734 (t80) REVERT: D 563 LEU cc_start: 0.9190 (tt) cc_final: 0.8859 (mp) outliers start: 40 outliers final: 31 residues processed: 295 average time/residue: 0.2337 time to fit residues: 111.4027 Evaluate side-chains 284 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 250 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 674 ILE Chi-restraints excluded: chain D residue 701 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 203 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 184 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 57 optimal weight: 0.0770 chunk 120 optimal weight: 10.0000 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 GLN B 410 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN D 410 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.126279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.103623 restraints weight = 86886.224| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.18 r_work: 0.3154 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17412 Z= 0.131 Angle : 0.477 4.715 23844 Z= 0.261 Chirality : 0.034 0.129 2952 Planarity : 0.003 0.031 2944 Dihedral : 3.990 17.025 2528 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.64 % Allowed : 11.50 % Favored : 85.86 % 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 are not related in a simple way. whole: -0.00 (0.17), residues: 2364 helix: 0.99 (0.13), residues: 1596 sheet: -2.23 (0.56), residues: 68 loop : -2.08 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 696 TYR 0.017 0.001 TYR D 564 PHE 0.014 0.001 PHE C 193 TRP 0.022 0.001 TRP D 380 HIS 0.004 0.001 HIS A 745 Details of bonding type rmsd covalent geometry : bond 0.00289 (17412) covalent geometry : angle 0.47699 (23844) hydrogen bonds : bond 0.03254 ( 1076) hydrogen bonds : angle 3.78314 ( 3144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Evaluate side-chains 310 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 273 time to evaluate : 0.940 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: B 155 PRO cc_start: 0.7735 (Cg_exo) cc_final: 0.7477 (Cg_endo) REVERT: D 155 PRO cc_start: 0.7830 (Cg_exo) cc_final: 0.7575 (Cg_endo) REVERT: D 419 MET cc_start: 0.8813 (mmt) cc_final: 0.8002 (mtt) REVERT: D 489 PHE cc_start: 0.6989 (t80) cc_final: 0.6677 (t80) REVERT: D 563 LEU cc_start: 0.9111 (tt) cc_final: 0.8800 (mp) outliers start: 37 outliers final: 31 residues processed: 298 average time/residue: 0.2275 time to fit residues: 111.1601 Evaluate side-chains 288 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 257 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 674 ILE Chi-restraints excluded: chain D residue 701 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 116 optimal weight: 0.9990 chunk 219 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 201 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 GLN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN A 279 GLN A 410 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.125520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.103040 restraints weight = 87003.356| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.17 r_work: 0.3143 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17412 Z= 0.156 Angle : 0.487 5.134 23844 Z= 0.268 Chirality : 0.034 0.127 2952 Planarity : 0.003 0.031 2944 Dihedral : 3.905 17.099 2528 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.21 % Allowed : 11.14 % Favored : 85.64 % 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 are not related in a simple way. whole: 0.25 (0.17), residues: 2364 helix: 1.25 (0.13), residues: 1596 sheet: -2.10 (0.52), residues: 92 loop : -2.13 (0.20), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 363 TYR 0.017 0.001 TYR D 564 PHE 0.013 0.001 PHE C 193 TRP 0.022 0.001 TRP C 380 HIS 0.003 0.001 HIS A 745 Details of bonding type rmsd covalent geometry : bond 0.00350 (17412) covalent geometry : angle 0.48742 (23844) hydrogen bonds : bond 0.03292 ( 1076) hydrogen bonds : angle 3.76540 ( 3144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Evaluate side-chains 311 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 266 time to evaluate : 1.162 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: B 155 PRO cc_start: 0.7733 (Cg_exo) cc_final: 0.7478 (Cg_endo) REVERT: B 419 MET cc_start: 0.8721 (mtt) cc_final: 0.8402 (mtt) REVERT: B 562 MET cc_start: 0.9071 (tpp) cc_final: 0.8596 (tpp) REVERT: C 419 MET cc_start: 0.8716 (mtt) cc_final: 0.8222 (mtt) REVERT: C 562 MET cc_start: 0.9027 (tpp) cc_final: 0.8789 (tpp) REVERT: A 419 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8145 (mtt) REVERT: A 562 MET cc_start: 0.8989 (tpp) cc_final: 0.8745 (tpp) REVERT: A 676 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8365 (mp) REVERT: D 155 PRO cc_start: 0.7764 (Cg_exo) cc_final: 0.7514 (Cg_endo) REVERT: D 419 MET cc_start: 0.8761 (mmt) cc_final: 0.8014 (mtt) REVERT: D 489 PHE cc_start: 0.7071 (t80) cc_final: 0.6741 (t80) REVERT: D 563 LEU cc_start: 0.9089 (tt) cc_final: 0.8793 (mp) outliers start: 45 outliers final: 37 residues processed: 296 average time/residue: 0.2399 time to fit residues: 116.7275 Evaluate side-chains 298 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 259 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 674 ILE Chi-restraints excluded: chain D residue 701 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 145 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 GLN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN A 279 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.101109 restraints weight = 87840.121| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.17 r_work: 0.3115 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17412 Z= 0.204 Angle : 0.528 5.491 23844 Z= 0.293 Chirality : 0.035 0.124 2952 Planarity : 0.003 0.032 2944 Dihedral : 4.036 18.354 2528 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.57 % Allowed : 11.79 % Favored : 84.64 % 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 are not related in a simple way. whole: 0.18 (0.17), residues: 2364 helix: 1.17 (0.13), residues: 1608 sheet: -2.09 (0.54), residues: 92 loop : -2.16 (0.20), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 225 TYR 0.018 0.002 TYR D 564 PHE 0.016 0.002 PHE C 316 TRP 0.024 0.002 TRP B 380 HIS 0.005 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00458 (17412) covalent geometry : angle 0.52830 (23844) hydrogen bonds : bond 0.03535 ( 1076) hydrogen bonds : angle 3.89727 ( 3144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Evaluate side-chains 310 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 260 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: B 155 PRO cc_start: 0.7760 (Cg_exo) cc_final: 0.7514 (Cg_endo) REVERT: C 419 MET cc_start: 0.8712 (mtt) cc_final: 0.8402 (mtt) REVERT: C 562 MET cc_start: 0.9009 (tpp) cc_final: 0.8737 (tpp) REVERT: C 676 LEU cc_start: 0.8394 (tt) cc_final: 0.8173 (tp) REVERT: A 419 MET cc_start: 0.8669 (mtt) cc_final: 0.8358 (mtt) REVERT: A 562 MET cc_start: 0.8986 (tpp) cc_final: 0.8719 (tpp) REVERT: A 676 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8462 (mp) REVERT: D 419 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8078 (mtt) REVERT: D 489 PHE cc_start: 0.7043 (t80) cc_final: 0.6722 (t80) REVERT: D 563 LEU cc_start: 0.9113 (tt) cc_final: 0.8817 (mp) outliers start: 50 outliers final: 44 residues processed: 292 average time/residue: 0.2323 time to fit residues: 112.1439 Evaluate side-chains 299 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 253 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 701 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 91 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 181 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 GLN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN A 279 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.125564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.103099 restraints weight = 86839.762| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.17 r_work: 0.3143 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17412 Z= 0.130 Angle : 0.470 5.596 23844 Z= 0.257 Chirality : 0.034 0.126 2952 Planarity : 0.003 0.030 2944 Dihedral : 3.762 16.182 2528 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.86 % Allowed : 12.79 % Favored : 84.36 % 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 are not related in a simple way. whole: 0.57 (0.17), residues: 2364 helix: 1.53 (0.13), residues: 1600 sheet: -2.07 (0.53), residues: 92 loop : -2.15 (0.20), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 363 TYR 0.017 0.001 TYR D 564 PHE 0.014 0.001 PHE C 193 TRP 0.023 0.001 TRP B 380 HIS 0.003 0.001 HIS A 745 Details of bonding type rmsd covalent geometry : bond 0.00286 (17412) covalent geometry : angle 0.46982 (23844) hydrogen bonds : bond 0.03126 ( 1076) hydrogen bonds : angle 3.67105 ( 3144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Evaluate side-chains 305 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 265 time to evaluate : 0.935 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: B 155 PRO cc_start: 0.7750 (Cg_exo) cc_final: 0.7502 (Cg_endo) REVERT: C 419 MET cc_start: 0.8708 (mtt) cc_final: 0.8410 (mtt) REVERT: A 419 MET cc_start: 0.8659 (mtt) cc_final: 0.8360 (mtt) REVERT: A 676 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8502 (mp) REVERT: D 155 PRO cc_start: 0.7763 (Cg_exo) cc_final: 0.7524 (Cg_endo) REVERT: D 419 MET cc_start: 0.8802 (mmt) cc_final: 0.8129 (mtt) REVERT: D 563 LEU cc_start: 0.9072 (tt) cc_final: 0.8784 (mp) outliers start: 40 outliers final: 36 residues processed: 292 average time/residue: 0.2239 time to fit residues: 108.3398 Evaluate side-chains 292 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 255 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 583 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 701 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 221 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 117 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 GLN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN A 279 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.122313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.099764 restraints weight = 87526.824| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.15 r_work: 0.3093 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.6555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 17412 Z= 0.258 Angle : 0.573 6.311 23844 Z= 0.320 Chirality : 0.037 0.128 2952 Planarity : 0.004 0.039 2944 Dihedral : 4.147 18.193 2528 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.14 % Allowed : 13.86 % Favored : 83.00 % 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 are not related in a simple way. whole: 0.17 (0.17), residues: 2364 helix: 1.19 (0.13), residues: 1608 sheet: -2.05 (0.54), residues: 92 loop : -2.28 (0.20), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 225 TYR 0.018 0.002 TYR D 564 PHE 0.018 0.002 PHE C 316 TRP 0.026 0.002 TRP D 380 HIS 0.005 0.002 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00581 (17412) covalent geometry : angle 0.57286 (23844) hydrogen bonds : bond 0.03735 ( 1076) hydrogen bonds : angle 4.02547 ( 3144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Evaluate side-chains 298 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 0.937 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: C 419 MET cc_start: 0.8740 (mtt) cc_final: 0.8464 (mtt) REVERT: A 419 MET cc_start: 0.8706 (mtt) cc_final: 0.8439 (mtt) REVERT: A 676 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8394 (mp) REVERT: D 419 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8197 (mtt) REVERT: D 489 PHE cc_start: 0.7074 (t80) cc_final: 0.6681 (t80) REVERT: D 563 LEU cc_start: 0.9131 (tt) cc_final: 0.8824 (mp) outliers start: 44 outliers final: 38 residues processed: 280 average time/residue: 0.2190 time to fit residues: 102.3367 Evaluate side-chains 294 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 254 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 701 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 91 optimal weight: 2.9990 chunk 191 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 9 optimal weight: 0.0970 chunk 206 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 GLN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN A 279 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.125844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.103451 restraints weight = 86354.320| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.17 r_work: 0.3155 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.6540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17412 Z= 0.103 Angle : 0.461 5.793 23844 Z= 0.250 Chirality : 0.033 0.131 2952 Planarity : 0.003 0.030 2944 Dihedral : 3.679 15.832 2528 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.93 % Allowed : 15.00 % Favored : 83.07 % 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 are not related in a simple way. whole: 0.74 (0.18), residues: 2364 helix: 1.61 (0.13), residues: 1604 sheet: -2.01 (0.54), residues: 92 loop : -1.97 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 696 TYR 0.017 0.001 TYR D 564 PHE 0.016 0.001 PHE C 193 TRP 0.031 0.001 TRP D 380 HIS 0.003 0.001 HIS A 745 Details of bonding type rmsd covalent geometry : bond 0.00230 (17412) covalent geometry : angle 0.46102 (23844) hydrogen bonds : bond 0.03040 ( 1076) hydrogen bonds : angle 3.62198 ( 3144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue ILE 123 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 LEU 139 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 MET 323 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 358 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 LEU 370 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 LEU 404 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 482 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 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 ILE 505 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 TYR 544 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 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 LEU 588 is missing expected H atoms. Skipping. Residue LYS 589 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 SER 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue SER 648 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 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 LEU 711 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue THR 740 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue THR 744 is missing expected H atoms. Skipping. Evaluate side-chains 292 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 265 time to evaluate : 0.717 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: B 155 PRO cc_start: 0.7737 (Cg_exo) cc_final: 0.7490 (Cg_endo) REVERT: B 216 GLN cc_start: 0.8549 (tt0) cc_final: 0.8300 (tt0) REVERT: B 599 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8448 (mp) REVERT: C 419 MET cc_start: 0.8714 (mtt) cc_final: 0.8478 (mtt) REVERT: A 419 MET cc_start: 0.8634 (mtt) cc_final: 0.8398 (mtt) REVERT: A 676 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8461 (mp) REVERT: D 155 PRO cc_start: 0.7780 (Cg_exo) cc_final: 0.7553 (Cg_endo) REVERT: D 419 MET cc_start: 0.8803 (mmt) cc_final: 0.8154 (mtt) REVERT: D 563 LEU cc_start: 0.9044 (tt) cc_final: 0.8757 (mp) outliers start: 27 outliers final: 22 residues processed: 283 average time/residue: 0.2162 time to fit residues: 100.7209 Evaluate side-chains 282 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 258 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 571 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 221 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 238 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 234 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 GLN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 GLN A 279 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.125717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.103406 restraints weight = 86712.597| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.17 r_work: 0.3151 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.6582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17412 Z= 0.116 Angle : 0.467 5.644 23844 Z= 0.253 Chirality : 0.033 0.143 2952 Planarity : 0.003 0.029 2944 Dihedral : 3.573 15.506 2528 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.93 % Allowed : 15.21 % Favored : 82.86 % 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 are not related in a simple way. whole: 0.92 (0.18), residues: 2364 helix: 1.75 (0.13), residues: 1604 sheet: -2.03 (0.53), residues: 92 loop : -1.88 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 363 TYR 0.017 0.001 TYR D 564 PHE 0.014 0.001 PHE C 193 TRP 0.032 0.001 TRP D 380 HIS 0.003 0.001 HIS C 745 Details of bonding type rmsd covalent geometry : bond 0.00257 (17412) covalent geometry : angle 0.46690 (23844) hydrogen bonds : bond 0.03021 ( 1076) hydrogen bonds : angle 3.54467 ( 3144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7745.79 seconds wall clock time: 131 minutes 56.49 seconds (7916.49 seconds total)