Starting phenix.real_space_refine on Fri Mar 6 12:35:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kzn_23083/03_2026/7kzn_23083.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kzn_23083/03_2026/7kzn_23083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kzn_23083/03_2026/7kzn_23083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kzn_23083/03_2026/7kzn_23083.map" model { file = "/net/cci-nas-00/data/ceres_data/7kzn_23083/03_2026/7kzn_23083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kzn_23083/03_2026/7kzn_23083.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 143 5.16 5 C 19545 2.51 5 N 5530 2.21 5 O 5987 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31205 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 1544 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 264} Link IDs: {'PTRANS': 19, 'TRANS': 295} Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1037 Unresolved non-hydrogen angles: 1346 Unresolved non-hydrogen dihedrals: 907 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLU:plan': 18, 'ARG:plan': 17, 'HIS:plan': 9, 'PHE:plan': 18, 'ASP:plan': 23, 'ASN:plan1': 15, 'TYR:plan': 12, 'TRP:plan': 10, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 626 Chain: "B" Number of atoms: 5028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5028 Classifications: {'peptide': 683} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PTRANS': 15, 'TRANS': 667} Chain breaks: 17 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 541 Unresolved non-hydrogen angles: 684 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'ASP:plan': 16, 'ARG:plan': 9, 'PHE:plan': 8, 'TYR:plan': 5, 'GLN:plan1': 8, 'GLU:plan': 10, 'HIS:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 293 Chain: "C" Number of atoms: 7293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7293 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PTRANS': 26, 'TRANS': 938} Chain breaks: 19 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 584 Unresolved non-hydrogen angles: 745 Unresolved non-hydrogen dihedrals: 483 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'ASP:plan': 11, 'ASN:plan1': 10, 'ARG:plan': 9, 'HIS:plan': 5, 'GLU:plan': 16, 'PHE:plan': 6, 'GLN:plan1': 4, 'TYR:plan': 5, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 302 Chain: "D" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3609 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 25, 'TRANS': 430} Chain breaks: 2 Chain: "E" Number of atoms: 3697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3697 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 24, 'TRANS': 449} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 495 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 1, 'TRANS': 98} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 437 Unresolved non-hydrogen dihedrals: 290 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 11, 'GLU:plan': 6, 'ARG:plan': 5, 'TYR:plan': 9, 'ASP:plan': 6, 'TRP:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 203 Chain: "G" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1089 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 1, 'TRANS': 136} Chain breaks: 1 Chain: "H" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 451 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 2, 'TRANS': 88} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 406 Unresolved non-hydrogen dihedrals: 281 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'TYR:plan': 8, 'GLU:plan': 5, 'PHE:plan': 4, 'GLN:plan1': 4, 'ASP:plan': 5, 'ARG:plan': 2, 'HIS:plan': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 175 Chain: "I" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 827 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "J" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 741 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "K" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 671 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "L" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 671 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "M" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 671 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "N" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 407 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 5, 'GLU:plan': 6, 'GLN:plan1': 3, 'TYR:plan': 5, 'PHE:plan': 5, 'ARG:plan': 2, 'HIS:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 167 Chain: "O" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 481 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 1, 'TRANS': 95} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 246 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 3, 'GLU:plan': 4, 'ASN:plan1': 9, 'GLN:plan1': 3, 'PHE:plan': 2, 'HIS:plan': 2, 'TRP:plan': 4, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 154 Chain: "P" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 805 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "X" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 605 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'TRANS': 120} Chain breaks: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 121 Planarities with less than four sites: {'UNK:plan-1': 121} Unresolved non-hydrogen planarities: 121 Chain: "Y" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 840 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 168} Link IDs: {'TRANS': 167} Chain breaks: 3 Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 504 Unresolved non-hydrogen dihedrals: 168 Planarities with less than four sites: {'UNK:plan-1': 168} Unresolved non-hydrogen planarities: 168 Chain: "Z" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Time building chain proxies: 6.17, per 1000 atoms: 0.20 Number of scatterers: 31205 At special positions: 0 Unit cell: (202.64, 224.4, 277.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 143 16.00 O 5987 8.00 N 5530 7.00 C 19545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.4 seconds 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8386 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 32 sheets defined 54.6% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 removed outlier: 4.385A pdb=" N TRP A 62 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 removed outlier: 3.667A pdb=" N VAL A 292 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY A 293 " --> pdb=" O ALA A 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 289 through 293' Processing helix chain 'B' and resid 17 through 33 removed outlier: 3.738A pdb=" N LYS B 33 " --> pdb=" O CYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 43 Processing helix chain 'B' and resid 45 through 56 removed outlier: 4.604A pdb=" N THR B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 125 removed outlier: 3.524A pdb=" N THR B 118 " --> pdb=" O ASN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 137 removed outlier: 3.532A pdb=" N LEU B 131 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 142 through 162 removed outlier: 4.020A pdb=" N LYS B 146 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 218 removed outlier: 4.826A pdb=" N TRP B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 255 Processing helix chain 'B' and resid 256 through 267 Processing helix chain 'B' and resid 272 through 299 removed outlier: 4.156A pdb=" N ALA B 276 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA B 286 " --> pdb=" O ARG B 282 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 337 removed outlier: 3.979A pdb=" N MET B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS B 326 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 363 removed outlier: 3.541A pdb=" N VAL B 345 " --> pdb=" O SER B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 405 removed outlier: 4.213A pdb=" N LYS B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 441 Processing helix chain 'B' and resid 454 through 475 Processing helix chain 'B' and resid 489 through 504 removed outlier: 3.930A pdb=" N ASP B 493 " --> pdb=" O GLN B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 514 Processing helix chain 'B' and resid 524 through 530 Processing helix chain 'B' and resid 541 through 570 removed outlier: 6.308A pdb=" N LYS B 547 " --> pdb=" O HIS B 543 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS B 548 " --> pdb=" O ASP B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 605 Proline residue: B 600 - end of helix Processing helix chain 'B' and resid 615 through 654 removed outlier: 4.391A pdb=" N GLU B 619 " --> pdb=" O GLU B 615 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS B 626 " --> pdb=" O ARG B 622 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 654 " --> pdb=" O SER B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 695 Processing helix chain 'B' and resid 730 through 742 Processing helix chain 'B' and resid 742 through 759 removed outlier: 3.685A pdb=" N ILE B 750 " --> pdb=" O ALA B 746 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N CYS B 751 " --> pdb=" O LEU B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 772 Processing helix chain 'B' and resid 774 through 784 Processing helix chain 'B' and resid 795 through 826 removed outlier: 3.675A pdb=" N LEU B 826 " --> pdb=" O THR B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 866 removed outlier: 4.023A pdb=" N ALA B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 906 Processing helix chain 'C' and resid 2 through 19 removed outlier: 3.715A pdb=" N ARG C 6 " --> pdb=" O ALA C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 31 removed outlier: 3.587A pdb=" N GLU C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 41 removed outlier: 3.668A pdb=" N PHE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 124 removed outlier: 3.561A pdb=" N LYS C 120 " --> pdb=" O LEU C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 137 removed outlier: 4.470A pdb=" N MET C 131 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 164 removed outlier: 4.003A pdb=" N ALA C 164 " --> pdb=" O THR C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 218 removed outlier: 3.627A pdb=" N THR C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLU C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TRP C 210 " --> pdb=" O CYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 254 removed outlier: 3.849A pdb=" N LEU C 236 " --> pdb=" O PRO C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 266 Processing helix chain 'C' and resid 272 through 300 removed outlier: 3.642A pdb=" N LEU C 300 " --> pdb=" O TYR C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 306 through 309 removed outlier: 3.771A pdb=" N GLN C 309 " --> pdb=" O PRO C 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 313 through 330 removed outlier: 3.805A pdb=" N GLU C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 339 through 362 Processing helix chain 'C' and resid 372 through 403 Processing helix chain 'C' and resid 414 through 440 removed outlier: 4.028A pdb=" N LEU C 430 " --> pdb=" O ALA C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 444 Processing helix chain 'C' and resid 454 through 467 removed outlier: 3.871A pdb=" N VAL C 466 " --> pdb=" O ILE C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 506 removed outlier: 4.025A pdb=" N ASP C 484 " --> pdb=" O ALA C 480 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU C 486 " --> pdb=" O ASP C 482 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 493 " --> pdb=" O ASN C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 527 removed outlier: 3.678A pdb=" N ALA C 516 " --> pdb=" O SER C 512 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET C 527 " --> pdb=" O PHE C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 535 Processing helix chain 'C' and resid 539 through 561 removed outlier: 4.120A pdb=" N ASN C 546 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 590 removed outlier: 3.766A pdb=" N ALA C 590 " --> pdb=" O ARG C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 639 removed outlier: 4.146A pdb=" N LYS C 618 " --> pdb=" O ASN C 614 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU C 624 " --> pdb=" O LEU C 620 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N HIS C 628 " --> pdb=" O GLU C 624 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS C 639 " --> pdb=" O ILE C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 677 removed outlier: 5.202A pdb=" N MET C 674 " --> pdb=" O ALA C 671 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLN C 675 " --> pdb=" O LYS C 672 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG C 676 " --> pdb=" O TYR C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 703 removed outlier: 3.663A pdb=" N THR C 703 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 700 through 703' Processing helix chain 'C' and resid 704 through 712 removed outlier: 3.932A pdb=" N GLU C 710 " --> pdb=" O VAL C 706 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS C 711 " --> pdb=" O ARG C 707 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL C 712 " --> pdb=" O GLU C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 715 No H-bonds generated for 'chain 'C' and resid 713 through 715' Processing helix chain 'C' and resid 725 through 735 removed outlier: 3.862A pdb=" N ASP C 729 " --> pdb=" O PRO C 725 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N MET C 730 " --> pdb=" O HIS C 726 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS C 733 " --> pdb=" O ASP C 729 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA C 735 " --> pdb=" O GLU C 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 772 removed outlier: 3.689A pdb=" N ARG C 761 " --> pdb=" O GLN C 757 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C 762 " --> pdb=" O GLY C 758 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG C 767 " --> pdb=" O GLU C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 787 removed outlier: 3.798A pdb=" N THR C 787 " --> pdb=" O ILE C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 837 removed outlier: 3.564A pdb=" N LYS C 812 " --> pdb=" O ARG C 808 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN C 813 " --> pdb=" O PHE C 809 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA C 814 " --> pdb=" O GLN C 810 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU C 815 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU C 829 " --> pdb=" O ARG C 825 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 833 " --> pdb=" O GLU C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 844 removed outlier: 3.831A pdb=" N GLU C 844 " --> pdb=" O GLU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 882 Processing helix chain 'C' and resid 915 through 935 removed outlier: 3.571A pdb=" N GLN C 935 " --> pdb=" O THR C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 979 Processing helix chain 'C' and resid 979 through 984 Processing helix chain 'C' and resid 994 through 1002 Processing helix chain 'C' and resid 1008 through 1031 Processing helix chain 'C' and resid 1042 through 1076 removed outlier: 3.790A pdb=" N LEU C1047 " --> pdb=" O LEU C1043 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C1056 " --> pdb=" O VAL C1052 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN C1065 " --> pdb=" O ASN C1061 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE C1076 " --> pdb=" O LEU C1072 " (cutoff:3.500A) Processing helix chain 'C' and resid 1091 through 1101 removed outlier: 3.922A pdb=" N LYS C1101 " --> pdb=" O MET C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1104 through 1121 Proline residue: C1116 - end of helix Processing helix chain 'C' and resid 1138 through 1159 removed outlier: 3.877A pdb=" N LEU C1149 " --> pdb=" O GLY C1145 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS C1150 " --> pdb=" O TRP C1146 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 221 Processing helix chain 'D' and resid 249 through 252 Processing helix chain 'D' and resid 253 through 270 removed outlier: 3.838A pdb=" N ASN D 270 " --> pdb=" O MET D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 282 removed outlier: 3.596A pdb=" N TRP D 282 " --> pdb=" O ASP D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 675 removed outlier: 3.518A pdb=" N LEU D 658 " --> pdb=" O LYS D 654 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU D 659 " --> pdb=" O PHE D 655 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU D 663 " --> pdb=" O GLU D 659 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA D 675 " --> pdb=" O ARG D 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 102 removed outlier: 3.864A pdb=" N ARG E 95 " --> pdb=" O GLU E 91 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS E 102 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 127 removed outlier: 4.381A pdb=" N VAL E 127 " --> pdb=" O GLN E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 190 Processing helix chain 'E' and resid 490 through 495 Processing helix chain 'E' and resid 497 through 499 No H-bonds generated for 'chain 'E' and resid 497 through 499' Processing helix chain 'E' and resid 500 through 517 removed outlier: 3.626A pdb=" N LEU E 509 " --> pdb=" O ARG E 505 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU E 510 " --> pdb=" O GLU E 506 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS E 511 " --> pdb=" O LYS E 507 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 549 Processing helix chain 'F' and resid 37 through 51 Processing helix chain 'F' and resid 59 through 76 Processing helix chain 'G' and resid 17 through 31 removed outlier: 3.712A pdb=" N ASP G 21 " --> pdb=" O ASP G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 50 Processing helix chain 'G' and resid 57 through 67 Processing helix chain 'G' and resid 75 through 90 removed outlier: 3.739A pdb=" N SER G 90 " --> pdb=" O ASN G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 104 removed outlier: 3.697A pdb=" N ALA G 102 " --> pdb=" O ASP G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 110 Processing helix chain 'G' and resid 117 through 128 removed outlier: 3.942A pdb=" N LEU G 121 " --> pdb=" O LEU G 117 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE G 128 " --> pdb=" O ILE G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 141 removed outlier: 3.620A pdb=" N LYS G 139 " --> pdb=" O ASP G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 158 Processing helix chain 'H' and resid 29 through 47 Processing helix chain 'H' and resid 49 through 61 Processing helix chain 'I' and resid 3 through 16 Processing helix chain 'I' and resid 38 through 64 removed outlier: 3.623A pdb=" N THR I 42 " --> pdb=" O ASP I 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 12 Processing helix chain 'J' and resid 39 through 60 Proline residue: J 48 - end of helix Processing helix chain 'K' and resid 16 through 34 removed outlier: 4.017A pdb=" N ASP K 22 " --> pdb=" O GLU K 18 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA K 30 " --> pdb=" O CYS K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 50 removed outlier: 3.922A pdb=" N ALA K 41 " --> pdb=" O GLU K 37 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS K 45 " --> pdb=" O ALA K 41 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE K 48 " --> pdb=" O ILE K 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 34 removed outlier: 4.558A pdb=" N GLN L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA L 30 " --> pdb=" O CYS L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 52 removed outlier: 4.561A pdb=" N LYS L 45 " --> pdb=" O ALA L 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 34 removed outlier: 4.048A pdb=" N ALA M 30 " --> pdb=" O CYS M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 52 removed outlier: 3.652A pdb=" N ILE M 40 " --> pdb=" O ILE M 36 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE M 48 " --> pdb=" O ILE M 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 34 removed outlier: 3.874A pdb=" N ASP N 25 " --> pdb=" O ALA N 21 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N THR N 28 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN N 29 " --> pdb=" O ASP N 25 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA N 30 " --> pdb=" O CYS N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 36 through 52 removed outlier: 3.702A pdb=" N GLU N 47 " --> pdb=" O TYR N 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 33 Processing helix chain 'O' and resid 39 through 41 No H-bonds generated for 'chain 'O' and resid 39 through 41' Processing helix chain 'O' and resid 42 through 62 removed outlier: 3.662A pdb=" N MET O 61 " --> pdb=" O ARG O 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 8 through 16 removed outlier: 3.911A pdb=" N PHE P 12 " --> pdb=" O ASP P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 27 through 45 Processing helix chain 'P' and resid 49 through 64 Processing helix chain 'X' and resid 321 through 345 removed outlier: 4.161A pdb=" N UNK X 329 " --> pdb=" O UNK X 325 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N UNK X 330 " --> pdb=" O UNK X 326 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N UNK X 345 " --> pdb=" O UNK X 341 " (cutoff:3.500A) Processing helix chain 'X' and resid 349 through 395 removed outlier: 3.528A pdb=" N UNK X 353 " --> pdb=" O UNK X 349 " (cutoff:3.500A) Processing helix chain 'X' and resid 404 through 448 Processing helix chain 'Y' and resid 271 through 278 Processing helix chain 'Y' and resid 285 through 294 removed outlier: 4.387A pdb=" N UNK Y 292 " --> pdb=" O UNK Y 288 " (cutoff:3.500A) Processing helix chain 'Y' and resid 295 through 383 removed outlier: 4.252A pdb=" N UNK Y 299 " --> pdb=" O UNK Y 295 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N UNK Y 301 " --> pdb=" O UNK Y 297 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N UNK Y 310 " --> pdb=" O UNK Y 306 " (cutoff:3.500A) Processing helix chain 'Y' and resid 395 through 410 Processing helix chain 'Y' and resid 425 through 444 Processing helix chain 'Z' and resid 7 through 27 removed outlier: 3.748A pdb=" N ALA Z 11 " --> pdb=" O ARG Z 7 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN Z 14 " --> pdb=" O TYR Z 10 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASN Z 17 " --> pdb=" O LYS Z 13 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU Z 18 " --> pdb=" O ASN Z 14 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG Z 21 " --> pdb=" O ASN Z 17 " (cutoff:3.500A) Processing helix chain 'Z' and resid 35 through 47 Processing helix chain 'Z' and resid 72 through 81 removed outlier: 3.582A pdb=" N THR Z 80 " --> pdb=" O GLN Z 76 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG Z 81 " --> pdb=" O THR Z 77 " (cutoff:3.500A) Processing helix chain 'Z' and resid 94 through 104 removed outlier: 4.048A pdb=" N VAL Z 98 " --> pdb=" O LEU Z 94 " (cutoff:3.500A) Processing helix chain 'Z' and resid 113 through 120 removed outlier: 3.880A pdb=" N MET Z 117 " --> pdb=" O LEU Z 113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 126 through 133 removed outlier: 3.712A pdb=" N GLN Z 132 " --> pdb=" O GLU Z 128 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 160 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 24 removed outlier: 5.927A pdb=" N GLY A 34 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N ASP A 48 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 82 Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 133 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 189 removed outlier: 4.225A pdb=" N LYS A 199 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU A 218 " --> pdb=" O LYS A 199 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU A 201 " --> pdb=" O HIS A 216 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N HIS A 216 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N MET A 203 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASP A 214 " --> pdb=" O MET A 203 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY A 205 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 239 Processing sheet with id=AA6, first strand: chain 'A' and resid 254 through 255 Processing sheet with id=AA7, first strand: chain 'A' and resid 298 through 302 Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 75 removed outlier: 3.703A pdb=" N ILE B 107 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 49 through 51 Processing sheet with id=AB1, first strand: chain 'D' and resid 181 through 185 removed outlier: 3.556A pdb=" N VAL L 68 " --> pdb=" O ARG D 184 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE M 85 " --> pdb=" O PHE M 78 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 193 through 200 removed outlier: 7.730A pdb=" N ASN K 63 " --> pdb=" O LYS P 74 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE P 76 " --> pdb=" O GLY K 61 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLY K 61 " --> pdb=" O PHE P 76 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TYR P 78 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE K 59 " --> pdb=" O TYR P 78 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE P 80 " --> pdb=" O HIS K 57 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N HIS K 57 " --> pdb=" O ILE P 80 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE K 85 " --> pdb=" O PHE K 78 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE K 75 " --> pdb=" O ALA K 13 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA K 13 " --> pdb=" O PHE K 75 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N TYR K 77 " --> pdb=" O LYS K 11 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 72 through 76 removed outlier: 7.732A pdb=" N HIS K 57 " --> pdb=" O ILE P 80 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE P 80 " --> pdb=" O HIS K 57 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE K 59 " --> pdb=" O TYR P 78 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TYR P 78 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLY K 61 " --> pdb=" O PHE P 76 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE P 76 " --> pdb=" O GLY K 61 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASN K 63 " --> pdb=" O LYS P 74 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU P 87 " --> pdb=" O THR P 24 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR P 24 " --> pdb=" O LEU P 87 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR P 89 " --> pdb=" O LYS P 22 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 297 through 302 removed outlier: 5.483A pdb=" N SER D 636 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ARG D 301 " --> pdb=" O VAL D 634 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL D 634 " --> pdb=" O ARG D 301 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 342 through 344 removed outlier: 4.013A pdb=" N ILE D 342 " --> pdb=" O PHE D 357 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE D 344 " --> pdb=" O TYR D 355 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR D 355 " --> pdb=" O ILE D 344 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 366 through 368 Processing sheet with id=AB7, first strand: chain 'D' and resid 416 through 418 removed outlier: 4.012A pdb=" N GLN D 427 " --> pdb=" O GLN D 418 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE D 448 " --> pdb=" O THR D 441 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 482 through 484 Processing sheet with id=AB9, first strand: chain 'D' and resid 523 through 527 removed outlier: 6.680A pdb=" N ALA D 539 " --> pdb=" O TYR D 524 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL D 526 " --> pdb=" O LEU D 537 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU D 537 " --> pdb=" O VAL D 526 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER D 540 " --> pdb=" O ASP D 544 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASP D 544 " --> pdb=" O SER D 540 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS D 545 " --> pdb=" O PHE D 561 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 567 through 572 removed outlier: 6.648A pdb=" N VAL D 583 " --> pdb=" O GLY D 568 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL D 570 " --> pdb=" O ALA D 581 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA D 581 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR D 584 " --> pdb=" O ARG D 588 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ARG D 588 " --> pdb=" O THR D 584 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 62 through 64 removed outlier: 4.684A pdb=" N TYR M 67 " --> pdb=" O CYS L 58 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N CYS L 58 " --> pdb=" O TYR M 67 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE L 85 " --> pdb=" O PHE L 78 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE L 75 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA L 13 " --> pdb=" O PHE L 75 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR L 77 " --> pdb=" O LYS L 11 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 152 through 154 removed outlier: 4.259A pdb=" N THR E 152 " --> pdb=" O VAL E 477 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL E 477 " --> pdb=" O THR E 152 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 163 through 169 removed outlier: 6.765A pdb=" N ALA E 181 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N VAL E 167 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL E 179 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR E 199 " --> pdb=" O VAL E 180 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 232 through 234 removed outlier: 3.931A pdb=" N ALA E 234 " --> pdb=" O ALA E 242 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA E 242 " --> pdb=" O ALA E 234 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 330 through 333 removed outlier: 3.928A pdb=" N ILE E 340 " --> pdb=" O LEU E 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 369 through 370 removed outlier: 3.851A pdb=" N ARG E 369 " --> pdb=" O LEU E 379 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 421 through 423 Processing sheet with id=AC9, first strand: chain 'F' and resid 83 through 93 Processing sheet with id=AD1, first strand: chain 'H' and resid 25 through 27 Processing sheet with id=AD2, first strand: chain 'I' and resid 22 through 25 removed outlier: 3.938A pdb=" N GLY J 19 " --> pdb=" O ILE J 92 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 57 through 61 Processing sheet with id=AD4, first strand: chain 'O' and resid 65 through 75 Processing sheet with id=AD5, first strand: chain 'Z' and resid 33 through 34 removed outlier: 4.017A pdb=" N ILE Z 70 " --> pdb=" O ILE Z 34 " (cutoff:3.500A) 1884 hydrogen bonds defined for protein. 5430 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: 6.47 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5648 1.32 - 1.44: 7793 1.44 - 1.57: 17958 1.57 - 1.70: 6 1.70 - 1.83: 233 Bond restraints: 31638 Sorted by residual: bond pdb=" CA SER D 314 " pdb=" CB SER D 314 " ideal model delta sigma weight residual 1.533 1.439 0.094 1.72e-02 3.38e+03 2.96e+01 bond pdb=" N LEU D 299 " pdb=" CA LEU D 299 " ideal model delta sigma weight residual 1.458 1.483 -0.025 6.30e-03 2.52e+04 1.55e+01 bond pdb=" C THR E 278 " pdb=" O THR E 278 " ideal model delta sigma weight residual 1.234 1.189 0.044 1.24e-02 6.50e+03 1.27e+01 bond pdb=" N VAL D 429 " pdb=" CA VAL D 429 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.14e-02 7.69e+03 1.23e+01 bond pdb=" N GLN D 427 " pdb=" CA GLN D 427 " ideal model delta sigma weight residual 1.454 1.497 -0.043 1.23e-02 6.61e+03 1.21e+01 ... (remaining 31633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 42098 4.20 - 8.39: 773 8.39 - 12.59: 74 12.59 - 16.78: 9 16.78 - 20.98: 2 Bond angle restraints: 42956 Sorted by residual: angle pdb=" CA PRO C 129 " pdb=" N PRO C 129 " pdb=" CD PRO C 129 " ideal model delta sigma weight residual 112.00 100.72 11.28 1.40e+00 5.10e-01 6.50e+01 angle pdb=" CB MET C 455 " pdb=" CG MET C 455 " pdb=" SD MET C 455 " ideal model delta sigma weight residual 112.70 91.72 20.98 3.00e+00 1.11e-01 4.89e+01 angle pdb=" CA ARG C 586 " pdb=" CB ARG C 586 " pdb=" CG ARG C 586 " ideal model delta sigma weight residual 114.10 127.85 -13.75 2.00e+00 2.50e-01 4.73e+01 angle pdb=" CB ARG B 603 " pdb=" CG ARG B 603 " pdb=" CD ARG B 603 " ideal model delta sigma weight residual 111.30 127.04 -15.74 2.30e+00 1.89e-01 4.68e+01 angle pdb=" N ARG D 184 " pdb=" CA ARG D 184 " pdb=" CB ARG D 184 " ideal model delta sigma weight residual 111.62 122.09 -10.47 1.62e+00 3.81e-01 4.18e+01 ... (remaining 42951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.51: 17183 18.51 - 37.03: 1587 37.03 - 55.54: 196 55.54 - 74.05: 43 74.05 - 92.57: 24 Dihedral angle restraints: 19033 sinusoidal: 6210 harmonic: 12823 Sorted by residual: dihedral pdb=" C THR D 313 " pdb=" N THR D 313 " pdb=" CA THR D 313 " pdb=" CB THR D 313 " ideal model delta harmonic sigma weight residual -122.00 -140.06 18.06 0 2.50e+00 1.60e-01 5.22e+01 dihedral pdb=" CA GLY E 473 " pdb=" C GLY E 473 " pdb=" N CYS E 474 " pdb=" CA CYS E 474 " ideal model delta harmonic sigma weight residual -180.00 -150.26 -29.74 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA CYS E 343 " pdb=" C CYS E 343 " pdb=" N ASN E 344 " pdb=" CA ASN E 344 " ideal model delta harmonic sigma weight residual 180.00 150.36 29.64 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 19030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 4678 0.130 - 0.261: 340 0.261 - 0.391: 27 0.391 - 0.522: 3 0.522 - 0.652: 3 Chirality restraints: 5051 Sorted by residual: chirality pdb=" CA THR D 313 " pdb=" N THR D 313 " pdb=" C THR D 313 " pdb=" CB THR D 313 " both_signs ideal model delta sigma weight residual False 2.53 1.87 0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CB ILE D 342 " pdb=" CA ILE D 342 " pdb=" CG1 ILE D 342 " pdb=" CG2 ILE D 342 " both_signs ideal model delta sigma weight residual False 2.64 2.01 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CB VAL D 558 " pdb=" CA VAL D 558 " pdb=" CG1 VAL D 558 " pdb=" CG2 VAL D 558 " both_signs ideal model delta sigma weight residual False -2.63 -2.05 -0.58 2.00e-01 2.50e+01 8.38e+00 ... (remaining 5048 not shown) Planarity restraints: 5639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 290 " -0.087 5.00e-02 4.00e+02 1.31e-01 2.73e+01 pdb=" N PRO D 291 " 0.226 5.00e-02 4.00e+02 pdb=" CA PRO D 291 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO D 291 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 755 " 0.041 2.00e-02 2.50e+03 3.88e-02 2.64e+01 pdb=" CG PHE C 755 " -0.087 2.00e-02 2.50e+03 pdb=" CD1 PHE C 755 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE C 755 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 755 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE C 755 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE C 755 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 230 " 0.021 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C ASN E 230 " -0.076 2.00e-02 2.50e+03 pdb=" O ASN E 230 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU E 231 " 0.026 2.00e-02 2.50e+03 ... (remaining 5636 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3795 2.74 - 3.28: 31638 3.28 - 3.82: 50095 3.82 - 4.36: 55191 4.36 - 4.90: 92503 Nonbonded interactions: 233222 Sorted by model distance: nonbonded pdb=" O SER D 304 " pdb=" OG SER D 307 " model vdw 2.202 3.040 nonbonded pdb=" ND2 ASN E 168 " pdb=" O ALA E 222 " model vdw 2.209 3.120 nonbonded pdb=" OG SER G 71 " pdb=" O CYS G 73 " model vdw 2.212 3.040 nonbonded pdb=" O ASP C 830 " pdb=" OG1 THR C 833 " model vdw 2.219 3.040 nonbonded pdb=" O GLN E 112 " pdb=" OG SER E 115 " model vdw 2.222 3.040 ... (remaining 233217 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'K' and ((resid 8 through 60 and (name N or name CA or name C or name O o \ r name CB )) or resid 61 or (resid 62 through 64 and (name N or name CA or name \ C or name O or name CB )) or resid 65 or (resid 66 through 80 and (name N or nam \ e CA or name C or name O or name CB )) or resid 81 or (resid 82 through 89 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'L' and ((resid 8 through 60 and (name N or name CA or name C or name O o \ r name CB )) or resid 61 or (resid 62 through 64 and (name N or name CA or name \ C or name O or name CB )) or resid 65 or (resid 66 through 80 and (name N or nam \ e CA or name C or name O or name CB )) or resid 81 or (resid 82 through 89 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'M' and ((resid 8 through 60 and (name N or name CA or name C or name O o \ r name CB )) or resid 61 or (resid 62 through 64 and (name N or name CA or name \ C or name O or name CB )) or resid 65 or (resid 66 through 80 and (name N or nam \ e CA or name C or name O or name CB )) or resid 81 or (resid 82 through 89 and ( \ name N or name CA or name C or name O or name CB )))) selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.040 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.120 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.135 31638 Z= 0.457 Angle : 1.357 20.981 42956 Z= 0.742 Chirality : 0.074 0.652 5051 Planarity : 0.010 0.131 5639 Dihedral : 14.785 92.568 10647 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.96 % Favored : 89.81 % Rotamer: Outliers : 0.48 % Allowed : 0.67 % Favored : 98.85 % Cbeta Deviations : 0.17 % 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: -3.22 (0.12), residues: 3985 helix: -1.15 (0.11), residues: 1866 sheet: -2.30 (0.22), residues: 500 loop : -3.23 (0.13), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.004 ARG G 44 TYR 0.061 0.005 TYR E 408 PHE 0.087 0.005 PHE C 755 TRP 0.055 0.006 TRP E 414 HIS 0.039 0.004 HIS L 70 Details of bonding type rmsd covalent geometry : bond 0.01016 (31638) covalent geometry : angle 1.35704 (42956) hydrogen bonds : bond 0.13702 ( 1879) hydrogen bonds : angle 6.85223 ( 5430) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 530 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.7066 (pmm) cc_final: 0.6696 (ttp) REVERT: B 290 GLU cc_start: 0.7679 (tp30) cc_final: 0.7381 (mm-30) REVERT: B 360 CYS cc_start: 0.7159 (m) cc_final: 0.6625 (m) REVERT: B 402 MET cc_start: 0.3651 (ttt) cc_final: 0.3165 (mtp) REVERT: B 503 GLU cc_start: 0.6719 (tm-30) cc_final: 0.6399 (tm-30) REVERT: B 628 TRP cc_start: 0.6161 (OUTLIER) cc_final: 0.4718 (m100) REVERT: B 802 MET cc_start: 0.5317 (mpp) cc_final: 0.4670 (mpp) REVERT: C 140 MET cc_start: 0.5939 (tpp) cc_final: 0.4415 (pmm) REVERT: C 152 THR cc_start: 0.6367 (p) cc_final: 0.6042 (p) REVERT: C 240 ARG cc_start: 0.7832 (mmm-85) cc_final: 0.7488 (tpp80) REVERT: C 328 MET cc_start: 0.5816 (mmp) cc_final: 0.5538 (ptm) REVERT: C 728 ASP cc_start: 0.5788 (t70) cc_final: 0.5481 (t70) REVERT: C 767 ARG cc_start: 0.5905 (ppt170) cc_final: 0.5547 (ptt90) REVERT: D 480 MET cc_start: 0.6567 (ppp) cc_final: 0.6231 (tmm) REVERT: D 627 VAL cc_start: 0.8884 (p) cc_final: 0.8536 (m) REVERT: D 648 LYS cc_start: 0.8645 (ptmt) cc_final: 0.8385 (mmtt) REVERT: E 207 ASN cc_start: 0.8176 (m110) cc_final: 0.7553 (p0) REVERT: E 223 LYS cc_start: 0.5562 (mptt) cc_final: 0.4374 (ttmt) REVERT: E 431 MET cc_start: 0.5429 (mmp) cc_final: 0.4031 (ttt) REVERT: G 103 PHE cc_start: 0.7807 (t80) cc_final: 0.7595 (t80) REVERT: G 112 LYS cc_start: 0.6433 (mmpt) cc_final: 0.5818 (mtmm) REVERT: G 113 THR cc_start: 0.7894 (p) cc_final: 0.7673 (p) REVERT: G 143 ARG cc_start: 0.7271 (mmp80) cc_final: 0.7054 (mmp80) REVERT: G 151 TYR cc_start: 0.5213 (m-10) cc_final: 0.4354 (m-80) REVERT: G 155 ARG cc_start: 0.8162 (mtp-110) cc_final: 0.7393 (mmt-90) REVERT: I 64 ASP cc_start: 0.6832 (t0) cc_final: 0.6621 (t0) REVERT: I 75 ARG cc_start: 0.7524 (mtp-110) cc_final: 0.7139 (mmm160) REVERT: J 45 ASP cc_start: 0.8178 (p0) cc_final: 0.7885 (p0) REVERT: K 19 MET cc_start: 0.8339 (ptt) cc_final: 0.8076 (ptt) REVERT: K 47 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6558 (tm-30) REVERT: K 59 ILE cc_start: 0.8433 (mt) cc_final: 0.8221 (mt) REVERT: M 32 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7552 (mp0) REVERT: P 43 GLU cc_start: 0.8099 (tp30) cc_final: 0.7885 (tp30) REVERT: Z 55 VAL cc_start: 0.8685 (t) cc_final: 0.8409 (p) REVERT: Z 75 PHE cc_start: 0.7885 (t80) cc_final: 0.7674 (t80) REVERT: Z 79 TYR cc_start: 0.8236 (t80) cc_final: 0.7923 (t80) REVERT: Z 131 MET cc_start: 0.8681 (mpp) cc_final: 0.8074 (mpp) outliers start: 13 outliers final: 4 residues processed: 540 average time/residue: 0.1850 time to fit residues: 159.7752 Evaluate side-chains 447 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 442 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 30.0000 chunk 424 optimal weight: 0.0010 chunk 155 optimal weight: 0.7980 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 GLN B 253 GLN ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 HIS C 403 GLN C 545 GLN C 546 ASN C 577 ASN C 666 GLN D 270 ASN D 409 ASN E 158 ASN E 189 GLN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN E 374 ASN G 65 GLN K 20 GLN ** M 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.126573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.108898 restraints weight = 76431.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.110129 restraints weight = 116828.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.110577 restraints weight = 79584.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.110917 restraints weight = 51512.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.111558 restraints weight = 43362.148| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 31638 Z= 0.158 Angle : 0.734 16.575 42956 Z= 0.388 Chirality : 0.045 0.215 5051 Planarity : 0.005 0.081 5639 Dihedral : 6.472 90.076 4596 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.17 % Favored : 93.78 % Rotamer: Outliers : 1.97 % Allowed : 11.33 % Favored : 86.71 % 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: -2.33 (0.12), residues: 3985 helix: -0.12 (0.11), residues: 1893 sheet: -1.94 (0.23), residues: 476 loop : -3.21 (0.13), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 34 TYR 0.025 0.002 TYR E 408 PHE 0.061 0.002 PHE B 390 TRP 0.037 0.002 TRP E 414 HIS 0.005 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00330 (31638) covalent geometry : angle 0.73424 (42956) hydrogen bonds : bond 0.05268 ( 1879) hydrogen bonds : angle 5.17462 ( 5430) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 505 time to evaluate : 1.023 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: B 398 ARG cc_start: 0.8009 (mtm180) cc_final: 0.6412 (tmt170) REVERT: B 628 TRP cc_start: 0.5833 (OUTLIER) cc_final: 0.5017 (m100) REVERT: C 140 MET cc_start: 0.5426 (tpp) cc_final: 0.4459 (pmm) REVERT: C 240 ARG cc_start: 0.7222 (mmm-85) cc_final: 0.6810 (tpp80) REVERT: C 728 ASP cc_start: 0.5614 (t70) cc_final: 0.5356 (t70) REVERT: C 730 MET cc_start: 0.7228 (mmm) cc_final: 0.6667 (tpp) REVERT: C 767 ARG cc_start: 0.5142 (ppt170) cc_final: 0.4463 (ttp80) REVERT: C 857 ARG cc_start: 0.6014 (tpt170) cc_final: 0.5809 (ttt-90) REVERT: C 1015 LYS cc_start: 0.7802 (mmtm) cc_final: 0.7412 (mtmt) REVERT: C 1072 LEU cc_start: 0.8924 (mm) cc_final: 0.8462 (pp) REVERT: D 479 CYS cc_start: 0.5795 (p) cc_final: 0.5592 (p) REVERT: D 585 ASP cc_start: 0.7905 (t70) cc_final: 0.7614 (t0) REVERT: E 194 MET cc_start: 0.6503 (ttm) cc_final: 0.6298 (ttt) REVERT: E 207 ASN cc_start: 0.7904 (m110) cc_final: 0.7438 (p0) REVERT: E 223 LYS cc_start: 0.5127 (mptt) cc_final: 0.4152 (ttmt) REVERT: E 227 LYS cc_start: 0.6457 (tptm) cc_final: 0.6216 (tptm) REVERT: E 431 MET cc_start: 0.5072 (mmp) cc_final: 0.4153 (ttt) REVERT: G 39 ASP cc_start: 0.6364 (t0) cc_final: 0.5924 (t0) REVERT: G 41 LYS cc_start: 0.8635 (mppt) cc_final: 0.8242 (mppt) REVERT: G 151 TYR cc_start: 0.5332 (m-10) cc_final: 0.4721 (m-80) REVERT: G 155 ARG cc_start: 0.7783 (mtp-110) cc_final: 0.7167 (mmt90) REVERT: I 45 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.7241 (m-10) REVERT: J 45 ASP cc_start: 0.7930 (p0) cc_final: 0.7604 (p0) REVERT: K 47 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6597 (tm-30) REVERT: P 53 THR cc_start: 0.8112 (p) cc_final: 0.7884 (t) REVERT: P 74 LYS cc_start: 0.7703 (tptt) cc_final: 0.7432 (mmtp) REVERT: Z 55 VAL cc_start: 0.8319 (t) cc_final: 0.8067 (p) REVERT: Z 76 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7381 (mm-40) outliers start: 53 outliers final: 26 residues processed: 534 average time/residue: 0.1883 time to fit residues: 159.0859 Evaluate side-chains 474 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 446 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 TRP Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 577 ASN Chi-restraints excluded: chain C residue 846 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 45 TYR Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain P residue 9 MET Chi-restraints excluded: chain Z residue 73 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 363 optimal weight: 30.0000 chunk 306 optimal weight: 20.0000 chunk 323 optimal weight: 0.8980 chunk 24 optimal weight: 40.0000 chunk 389 optimal weight: 20.0000 chunk 36 optimal weight: 50.0000 chunk 227 optimal weight: 0.6980 chunk 145 optimal weight: 7.9990 chunk 231 optimal weight: 5.9990 chunk 291 optimal weight: 9.9990 chunk 281 optimal weight: 0.2980 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 GLN C 267 HIS C 515 HIS C 869 GLN D 270 ASN ** D 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 GLN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN M 52 HIS ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.123416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.107468 restraints weight = 76144.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.108327 restraints weight = 144739.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.109163 restraints weight = 90536.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.108908 restraints weight = 70565.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.109544 restraints weight = 54726.901| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 31638 Z= 0.243 Angle : 0.779 19.801 42956 Z= 0.413 Chirality : 0.047 0.197 5051 Planarity : 0.006 0.073 5639 Dihedral : 6.411 80.871 4595 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.11 % Favored : 90.84 % Rotamer: Outliers : 3.38 % Allowed : 16.93 % Favored : 79.69 % 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: -2.19 (0.13), residues: 3985 helix: 0.07 (0.11), residues: 1894 sheet: -1.99 (0.22), residues: 517 loop : -3.22 (0.13), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 682 TYR 0.040 0.003 TYR E 408 PHE 0.035 0.003 PHE E 422 TRP 0.027 0.003 TRP E 434 HIS 0.011 0.002 HIS D 590 Details of bonding type rmsd covalent geometry : bond 0.00550 (31638) covalent geometry : angle 0.77913 (42956) hydrogen bonds : bond 0.05301 ( 1879) hydrogen bonds : angle 5.19271 ( 5430) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 475 time to evaluate : 1.008 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: B 398 ARG cc_start: 0.7966 (mtm180) cc_final: 0.6499 (tmt170) REVERT: B 628 TRP cc_start: 0.5840 (OUTLIER) cc_final: 0.4945 (m100) REVERT: B 802 MET cc_start: 0.5116 (mpp) cc_final: 0.4294 (mpp) REVERT: C 140 MET cc_start: 0.5378 (tpp) cc_final: 0.4516 (pmm) REVERT: C 240 ARG cc_start: 0.7093 (mmm-85) cc_final: 0.6658 (tpp80) REVERT: C 455 MET cc_start: 0.5530 (ppp) cc_final: 0.4944 (ppp) REVERT: C 559 GLU cc_start: 0.6581 (tp30) cc_final: 0.6263 (tp30) REVERT: C 728 ASP cc_start: 0.5900 (t70) cc_final: 0.5317 (t70) REVERT: C 767 ARG cc_start: 0.5470 (ppt170) cc_final: 0.4994 (ttp80) REVERT: C 855 LEU cc_start: 0.6957 (tp) cc_final: 0.6710 (tp) REVERT: C 1072 LEU cc_start: 0.8806 (mm) cc_final: 0.8414 (pp) REVERT: D 184 ARG cc_start: 0.5608 (mtt-85) cc_final: 0.5350 (mtt180) REVERT: D 480 MET cc_start: 0.6592 (ppp) cc_final: 0.6256 (tmm) REVERT: E 223 LYS cc_start: 0.5459 (mptt) cc_final: 0.4367 (ttmt) REVERT: E 227 LYS cc_start: 0.6450 (tptm) cc_final: 0.5829 (pptt) REVERT: E 431 MET cc_start: 0.5056 (mmp) cc_final: 0.4013 (ttt) REVERT: E 437 TYR cc_start: 0.6406 (OUTLIER) cc_final: 0.5364 (p90) REVERT: G 39 ASP cc_start: 0.6339 (t0) cc_final: 0.5934 (t0) REVERT: G 41 LYS cc_start: 0.8526 (mppt) cc_final: 0.8299 (mppt) REVERT: G 151 TYR cc_start: 0.5326 (m-10) cc_final: 0.4709 (m-80) REVERT: G 155 ARG cc_start: 0.7661 (mtp-110) cc_final: 0.7119 (mmt90) REVERT: I 76 SER cc_start: 0.8633 (p) cc_final: 0.8420 (m) REVERT: J 8 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7599 (mm) REVERT: K 47 GLU cc_start: 0.7048 (tm-30) cc_final: 0.6511 (tm-30) REVERT: M 20 GLN cc_start: 0.7076 (tp40) cc_final: 0.6839 (tp40) REVERT: P 21 VAL cc_start: 0.7830 (OUTLIER) cc_final: 0.7537 (m) REVERT: P 74 LYS cc_start: 0.7569 (tptt) cc_final: 0.7278 (tppp) REVERT: Z 55 VAL cc_start: 0.8228 (t) cc_final: 0.7973 (p) REVERT: Z 76 GLN cc_start: 0.7486 (mm-40) cc_final: 0.7223 (mm-40) outliers start: 91 outliers final: 59 residues processed: 529 average time/residue: 0.1816 time to fit residues: 153.6594 Evaluate side-chains 512 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 449 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 TRP Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 816 LYS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 1010 PHE Chi-restraints excluded: chain C residue 1041 HIS Chi-restraints excluded: chain D residue 258 HIS Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 414 TRP Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 437 TYR Chi-restraints excluded: chain E residue 495 ILE Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 94 TYR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain L residue 67 TYR Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain P residue 9 MET Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain Z residue 73 LEU Chi-restraints excluded: chain Z residue 158 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 300 optimal weight: 9.9990 chunk 320 optimal weight: 2.9990 chunk 30 optimal weight: 50.0000 chunk 382 optimal weight: 7.9990 chunk 100 optimal weight: 50.0000 chunk 307 optimal weight: 8.9990 chunk 26 optimal weight: 50.0000 chunk 288 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 308 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 568 HIS C 515 HIS C 570 ASN C 780 ASN C 869 GLN D 270 ASN ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 HIS E 337 GLN ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 44 GLN ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 160 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.119611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.101910 restraints weight = 77411.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.102854 restraints weight = 140683.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.103864 restraints weight = 86747.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.103723 restraints weight = 62896.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.104353 restraints weight = 51083.594| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.155 31638 Z= 0.391 Angle : 0.958 24.047 42956 Z= 0.509 Chirality : 0.054 0.262 5051 Planarity : 0.007 0.083 5639 Dihedral : 7.009 77.302 4595 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.69 % Favored : 88.26 % Rotamer: Outliers : 5.72 % Allowed : 20.39 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.62 (0.12), residues: 3985 helix: -0.31 (0.11), residues: 1892 sheet: -2.24 (0.22), residues: 516 loop : -3.37 (0.13), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 767 TYR 0.060 0.004 TYR E 408 PHE 0.038 0.004 PHE C 755 TRP 0.033 0.004 TRP E 434 HIS 0.020 0.003 HIS D 590 Details of bonding type rmsd covalent geometry : bond 0.00889 (31638) covalent geometry : angle 0.95766 (42956) hydrogen bonds : bond 0.06169 ( 1879) hydrogen bonds : angle 5.66494 ( 5430) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 459 time to evaluate : 0.856 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: B 398 ARG cc_start: 0.8019 (mtm180) cc_final: 0.6521 (tmt170) REVERT: B 503 GLU cc_start: 0.6741 (tm-30) cc_final: 0.6335 (tm-30) REVERT: B 560 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6880 (tp) REVERT: B 568 HIS cc_start: 0.6988 (OUTLIER) cc_final: 0.5982 (t70) REVERT: B 615 GLU cc_start: 0.5128 (OUTLIER) cc_final: 0.4430 (pm20) REVERT: B 628 TRP cc_start: 0.6223 (OUTLIER) cc_final: 0.5231 (m100) REVERT: B 683 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.6978 (tt) REVERT: C 140 MET cc_start: 0.5941 (tpp) cc_final: 0.4477 (pmm) REVERT: C 240 ARG cc_start: 0.7034 (mmm-85) cc_final: 0.6791 (tpp80) REVERT: C 243 MET cc_start: 0.7050 (mmm) cc_final: 0.6386 (tpp) REVERT: C 455 MET cc_start: 0.5234 (ppp) cc_final: 0.4875 (ppp) REVERT: C 491 GLN cc_start: 0.7071 (pm20) cc_final: 0.6692 (pm20) REVERT: C 687 MET cc_start: 0.5060 (tpp) cc_final: 0.3828 (mmm) REVERT: C 728 ASP cc_start: 0.6839 (OUTLIER) cc_final: 0.5832 (t70) REVERT: C 730 MET cc_start: 0.7523 (mmm) cc_final: 0.7203 (tpp) REVERT: C 767 ARG cc_start: 0.6240 (ppt170) cc_final: 0.5929 (ptt90) REVERT: C 915 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7279 (mt) REVERT: D 184 ARG cc_start: 0.6105 (mtt-85) cc_final: 0.5898 (mtt180) REVERT: D 290 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7747 (ptt-90) REVERT: E 182 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.6882 (m-80) REVERT: E 223 LYS cc_start: 0.5812 (mptt) cc_final: 0.4356 (tttm) REVERT: E 227 LYS cc_start: 0.6394 (tptm) cc_final: 0.5817 (pptt) REVERT: E 391 GLU cc_start: 0.5944 (tt0) cc_final: 0.4094 (pm20) REVERT: E 414 TRP cc_start: 0.7418 (OUTLIER) cc_final: 0.6145 (m100) REVERT: E 431 MET cc_start: 0.5439 (mmp) cc_final: 0.4283 (ttt) REVERT: E 437 TYR cc_start: 0.6567 (OUTLIER) cc_final: 0.5196 (p90) REVERT: G 151 TYR cc_start: 0.5376 (m-10) cc_final: 0.4864 (m-80) REVERT: G 155 ARG cc_start: 0.7719 (mtp-110) cc_final: 0.7118 (mmt90) REVERT: I 64 ASP cc_start: 0.7523 (t0) cc_final: 0.6997 (t0) REVERT: I 94 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.8022 (p90) REVERT: J 8 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7678 (mm) REVERT: J 45 ASP cc_start: 0.7883 (p0) cc_final: 0.7551 (p0) REVERT: J 64 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7615 (mt0) REVERT: K 47 GLU cc_start: 0.7016 (tm-30) cc_final: 0.6497 (tm-30) REVERT: L 45 LYS cc_start: 0.7143 (pttm) cc_final: 0.6697 (pttm) REVERT: L 48 PHE cc_start: 0.6437 (OUTLIER) cc_final: 0.6156 (t80) REVERT: L 62 ARG cc_start: 0.6143 (OUTLIER) cc_final: 0.5941 (mtt-85) REVERT: L 74 HIS cc_start: 0.6684 (OUTLIER) cc_final: 0.6300 (m90) REVERT: P 21 VAL cc_start: 0.7891 (OUTLIER) cc_final: 0.7652 (m) REVERT: P 30 MET cc_start: 0.7838 (tpp) cc_final: 0.7207 (tpt) REVERT: Z 76 GLN cc_start: 0.7602 (mm-40) cc_final: 0.7344 (mm-40) outliers start: 154 outliers final: 99 residues processed: 568 average time/residue: 0.1829 time to fit residues: 165.3919 Evaluate side-chains 546 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 429 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 TRP Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 816 LYS Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 728 ASP Chi-restraints excluded: chain C residue 773 THR Chi-restraints excluded: chain C residue 846 VAL Chi-restraints excluded: chain C residue 915 LEU Chi-restraints excluded: chain C residue 924 GLN Chi-restraints excluded: chain C residue 925 CYS Chi-restraints excluded: chain C residue 1010 PHE Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 258 HIS Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 325 PHE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 413 TRP Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 481 ASP Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 555 LYS Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain D residue 614 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 182 TYR Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 291 TRP Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 414 TRP Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 437 TYR Chi-restraints excluded: chain E residue 450 SER Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 476 SER Chi-restraints excluded: chain E residue 495 ILE Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 44 GLN Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 94 TYR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 48 PHE Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 64 PHE Chi-restraints excluded: chain L residue 67 TYR Chi-restraints excluded: chain L residue 74 HIS Chi-restraints excluded: chain L residue 79 TYR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain P residue 9 MET Chi-restraints excluded: chain P residue 19 THR Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Z residue 73 LEU Chi-restraints excluded: chain Z residue 95 PHE Chi-restraints excluded: chain Z residue 158 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 40 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 292 optimal weight: 40.0000 chunk 303 optimal weight: 0.9980 chunk 269 optimal weight: 0.7980 chunk 124 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 356 optimal weight: 8.9990 chunk 244 optimal weight: 0.4980 chunk 376 optimal weight: 4.9990 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS C 570 ASN D 270 ASN ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.122395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.106113 restraints weight = 76933.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.106828 restraints weight = 151295.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.107721 restraints weight = 91658.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.107649 restraints weight = 66162.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.108172 restraints weight = 53894.030| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 31638 Z= 0.224 Angle : 0.773 20.744 42956 Z= 0.407 Chirality : 0.047 0.241 5051 Planarity : 0.005 0.067 5639 Dihedral : 6.462 84.302 4595 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.88 % Favored : 91.07 % Rotamer: Outliers : 5.64 % Allowed : 22.58 % Favored : 71.78 % 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: -2.27 (0.13), residues: 3985 helix: 0.06 (0.11), residues: 1901 sheet: -2.14 (0.22), residues: 505 loop : -3.31 (0.13), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 956 TYR 0.036 0.002 TYR E 408 PHE 0.030 0.002 PHE E 422 TRP 0.032 0.003 TRP D 440 HIS 0.016 0.002 HIS B 568 Details of bonding type rmsd covalent geometry : bond 0.00504 (31638) covalent geometry : angle 0.77266 (42956) hydrogen bonds : bond 0.05226 ( 1879) hydrogen bonds : angle 5.21300 ( 5430) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 471 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 266 LEU cc_start: 0.7071 (mt) cc_final: 0.6718 (mt) REVERT: B 398 ARG cc_start: 0.7962 (mtm180) cc_final: 0.6468 (tmt170) REVERT: B 560 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6667 (tp) REVERT: B 615 GLU cc_start: 0.5022 (OUTLIER) cc_final: 0.4585 (pm20) REVERT: B 628 TRP cc_start: 0.6204 (OUTLIER) cc_final: 0.5127 (m100) REVERT: B 745 SER cc_start: 0.6277 (m) cc_final: 0.6016 (p) REVERT: C 140 MET cc_start: 0.5855 (tpp) cc_final: 0.4563 (pmm) REVERT: C 240 ARG cc_start: 0.7168 (mmm-85) cc_final: 0.6902 (tpp80) REVERT: C 243 MET cc_start: 0.6984 (mmm) cc_final: 0.6295 (tpp) REVERT: C 455 MET cc_start: 0.5429 (ppp) cc_final: 0.4962 (ppp) REVERT: C 491 GLN cc_start: 0.6964 (pm20) cc_final: 0.6736 (pm20) REVERT: C 674 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7317 (mmm) REVERT: C 728 ASP cc_start: 0.6270 (t70) cc_final: 0.5954 (t70) REVERT: C 730 MET cc_start: 0.7388 (mmm) cc_final: 0.7073 (tpp) REVERT: C 767 ARG cc_start: 0.5671 (ppt170) cc_final: 0.5338 (ptt90) REVERT: C 1015 LYS cc_start: 0.7820 (mmtm) cc_final: 0.7327 (mtmt) REVERT: C 1072 LEU cc_start: 0.8853 (mm) cc_final: 0.8480 (pp) REVERT: D 290 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7758 (ptt-90) REVERT: E 207 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7388 (p0) REVERT: E 223 LYS cc_start: 0.5091 (mptt) cc_final: 0.4011 (ttmt) REVERT: E 227 LYS cc_start: 0.6665 (tptm) cc_final: 0.5813 (pptt) REVERT: E 345 ARG cc_start: 0.6521 (OUTLIER) cc_final: 0.5557 (ptt180) REVERT: E 391 GLU cc_start: 0.6121 (tt0) cc_final: 0.4136 (pm20) REVERT: E 431 MET cc_start: 0.5127 (mmp) cc_final: 0.4000 (ttt) REVERT: E 437 TYR cc_start: 0.6455 (OUTLIER) cc_final: 0.5198 (p90) REVERT: G 103 PHE cc_start: 0.6666 (t80) cc_final: 0.5957 (t80) REVERT: G 151 TYR cc_start: 0.5295 (m-10) cc_final: 0.4589 (m-80) REVERT: G 155 ARG cc_start: 0.7721 (mtp-110) cc_final: 0.7103 (mmt90) REVERT: I 64 ASP cc_start: 0.7449 (t0) cc_final: 0.6777 (t0) REVERT: I 94 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7625 (p90) REVERT: J 8 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7427 (mm) REVERT: J 64 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7528 (mt0) REVERT: K 47 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6640 (tm-30) REVERT: L 48 PHE cc_start: 0.6442 (OUTLIER) cc_final: 0.6125 (t80) REVERT: L 62 ARG cc_start: 0.6151 (OUTLIER) cc_final: 0.5809 (mtt-85) REVERT: L 82 GLN cc_start: 0.6533 (tp-100) cc_final: 0.5342 (mm110) REVERT: P 21 VAL cc_start: 0.7818 (OUTLIER) cc_final: 0.7542 (m) REVERT: P 53 THR cc_start: 0.8145 (p) cc_final: 0.7899 (t) REVERT: P 79 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6914 (tm-30) REVERT: P 95 ARG cc_start: 0.6834 (ttm110) cc_final: 0.6631 (ttm110) REVERT: Z 76 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7378 (mm-40) REVERT: Z 79 TYR cc_start: 0.7668 (t80) cc_final: 0.7277 (t80) outliers start: 152 outliers final: 102 residues processed: 576 average time/residue: 0.1867 time to fit residues: 171.3234 Evaluate side-chains 568 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 452 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 TRP Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 690 PHE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 816 LYS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 747 ASN Chi-restraints excluded: chain C residue 846 VAL Chi-restraints excluded: chain C residue 924 GLN Chi-restraints excluded: chain C residue 925 CYS Chi-restraints excluded: chain C residue 1010 PHE Chi-restraints excluded: chain C residue 1041 HIS Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 258 HIS Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 290 ARG Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 325 PHE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 413 TRP Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 590 HIS Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 158 ASN Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 291 TRP Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 345 ARG Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 414 TRP Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 437 TYR Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 495 ILE Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 94 TYR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 48 PHE Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 67 TYR Chi-restraints excluded: chain L residue 79 TYR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain P residue 9 MET Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Z residue 73 LEU Chi-restraints excluded: chain Z residue 158 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 163 optimal weight: 0.0670 chunk 279 optimal weight: 0.8980 chunk 118 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 294 optimal weight: 40.0000 chunk 322 optimal weight: 5.9990 chunk 331 optimal weight: 0.0010 chunk 292 optimal weight: 40.0000 chunk 155 optimal weight: 0.2980 chunk 199 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.6526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 325 ASN ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS C 545 GLN C 570 ASN C 869 GLN D 270 ASN ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN E 189 GLN G 109 ASN K 20 GLN L 53 ASN ** L 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 GLN ** Z 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.126631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.109257 restraints weight = 75541.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.110155 restraints weight = 123676.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.110923 restraints weight = 82419.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.111147 restraints weight = 53374.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.111827 restraints weight = 44324.425| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31638 Z= 0.139 Angle : 0.673 17.687 42956 Z= 0.349 Chirality : 0.043 0.209 5051 Planarity : 0.005 0.071 5639 Dihedral : 5.733 87.164 4595 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.32 % Favored : 93.65 % Rotamer: Outliers : 4.34 % Allowed : 24.25 % Favored : 71.41 % 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: -1.71 (0.13), residues: 3985 helix: 0.57 (0.12), residues: 1909 sheet: -1.90 (0.23), residues: 490 loop : -3.10 (0.13), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 217 TYR 0.019 0.002 TYR C 673 PHE 0.018 0.002 PHE I 71 TRP 0.034 0.002 TRP B 589 HIS 0.009 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00289 (31638) covalent geometry : angle 0.67265 (42956) hydrogen bonds : bond 0.04356 ( 1879) hydrogen bonds : angle 4.70639 ( 5430) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 491 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 266 LEU cc_start: 0.7035 (mt) cc_final: 0.6750 (mt) REVERT: B 402 MET cc_start: 0.4450 (OUTLIER) cc_final: 0.2373 (mtp) REVERT: B 560 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6237 (tp) REVERT: B 628 TRP cc_start: 0.5785 (OUTLIER) cc_final: 0.4849 (m100) REVERT: B 802 MET cc_start: 0.5042 (mpp) cc_final: 0.4165 (mpp) REVERT: C 140 MET cc_start: 0.5580 (tpp) cc_final: 0.4589 (pmm) REVERT: C 240 ARG cc_start: 0.7350 (mmm-85) cc_final: 0.6980 (tpp80) REVERT: C 243 MET cc_start: 0.6777 (mmm) cc_final: 0.6403 (mmm) REVERT: C 455 MET cc_start: 0.5567 (ppp) cc_final: 0.4931 (ppp) REVERT: C 570 ASN cc_start: 0.6657 (OUTLIER) cc_final: 0.6138 (t0) REVERT: C 687 MET cc_start: 0.4908 (tpp) cc_final: 0.3938 (mmm) REVERT: C 1015 LYS cc_start: 0.7920 (mmtm) cc_final: 0.7410 (mtmt) REVERT: C 1072 LEU cc_start: 0.9009 (mm) cc_final: 0.8604 (pp) REVERT: D 481 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7520 (m-30) REVERT: D 535 MET cc_start: 0.7228 (mmt) cc_final: 0.6905 (mmp) REVERT: D 586 ASP cc_start: 0.6851 (m-30) cc_final: 0.6641 (m-30) REVERT: D 598 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7735 (mmtm) REVERT: E 207 ASN cc_start: 0.7890 (m110) cc_final: 0.7645 (p0) REVERT: E 211 TYR cc_start: 0.5551 (m-80) cc_final: 0.5330 (m-80) REVERT: E 223 LYS cc_start: 0.4982 (mptt) cc_final: 0.3884 (ttmt) REVERT: E 227 LYS cc_start: 0.6595 (tptm) cc_final: 0.5389 (pptt) REVERT: E 273 GLN cc_start: 0.6771 (OUTLIER) cc_final: 0.6173 (tm-30) REVERT: E 391 GLU cc_start: 0.5564 (tt0) cc_final: 0.4174 (pm20) REVERT: E 431 MET cc_start: 0.4899 (mmp) cc_final: 0.3788 (ttt) REVERT: E 437 TYR cc_start: 0.6393 (OUTLIER) cc_final: 0.5585 (p90) REVERT: G 89 MET cc_start: 0.7846 (tpt) cc_final: 0.7618 (mmt) REVERT: G 103 PHE cc_start: 0.6504 (t80) cc_final: 0.5881 (t80) REVERT: G 151 TYR cc_start: 0.5194 (m-10) cc_final: 0.4693 (m-80) REVERT: G 155 ARG cc_start: 0.7890 (mtp-110) cc_final: 0.7182 (mmt90) REVERT: I 94 TYR cc_start: 0.7937 (OUTLIER) cc_final: 0.7413 (p90) REVERT: J 45 ASP cc_start: 0.8276 (p0) cc_final: 0.7961 (p0) REVERT: J 64 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7559 (mt0) REVERT: K 47 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6824 (tm-30) REVERT: K 67 TYR cc_start: 0.5032 (OUTLIER) cc_final: 0.3470 (t80) REVERT: L 48 PHE cc_start: 0.6189 (OUTLIER) cc_final: 0.5795 (t80) REVERT: L 82 GLN cc_start: 0.6459 (tp-100) cc_final: 0.5146 (mm110) REVERT: M 19 MET cc_start: 0.6553 (ptm) cc_final: 0.5740 (tmm) REVERT: P 21 VAL cc_start: 0.7275 (OUTLIER) cc_final: 0.6968 (m) REVERT: P 53 THR cc_start: 0.8040 (p) cc_final: 0.7747 (t) REVERT: P 95 ARG cc_start: 0.6987 (ttm110) cc_final: 0.6715 (ttm110) REVERT: Z 58 MET cc_start: 0.3067 (pmm) cc_final: 0.2000 (ppp) REVERT: Z 83 ARG cc_start: 0.3984 (mpp-170) cc_final: 0.3331 (mpp-170) REVERT: Z 133 LEU cc_start: 0.8265 (mt) cc_final: 0.7944 (mt) outliers start: 117 outliers final: 63 residues processed: 567 average time/residue: 0.1850 time to fit residues: 167.3891 Evaluate side-chains 531 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 455 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 TRP Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 690 PHE Chi-restraints excluded: chain B residue 816 LYS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 491 GLN Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 570 ASN Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 846 VAL Chi-restraints excluded: chain C residue 925 CYS Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1010 PHE Chi-restraints excluded: chain C residue 1041 HIS Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 481 ASP Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 590 HIS Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 627 VAL Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 291 TRP Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 414 TRP Chi-restraints excluded: chain E residue 437 TYR Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 94 TYR Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain K residue 67 TYR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain L residue 48 PHE Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 79 TYR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain M residue 79 TYR Chi-restraints excluded: chain P residue 9 MET Chi-restraints excluded: chain P residue 19 THR Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain Z residue 73 LEU Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 158 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 396 optimal weight: 20.0000 chunk 289 optimal weight: 30.0000 chunk 281 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 198 optimal weight: 8.9990 chunk 364 optimal weight: 30.0000 chunk 191 optimal weight: 30.0000 chunk 103 optimal weight: 50.0000 chunk 22 optimal weight: 30.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS C 869 GLN D 270 ASN ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 GLN ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 155 HIS ** 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 = 0.4121 r_free = 0.4121 target = 0.123444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.108165 restraints weight = 76308.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.109146 restraints weight = 164651.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.109911 restraints weight = 95028.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.109707 restraints weight = 72547.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.110211 restraints weight = 56621.625| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 31638 Z= 0.305 Angle : 0.846 22.178 42956 Z= 0.445 Chirality : 0.050 0.229 5051 Planarity : 0.006 0.070 5639 Dihedral : 6.251 76.836 4592 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.54 % Favored : 89.39 % Rotamer: Outliers : 5.46 % Allowed : 24.17 % Favored : 70.37 % 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: -2.05 (0.13), residues: 3985 helix: 0.28 (0.11), residues: 1906 sheet: -2.11 (0.22), residues: 521 loop : -3.24 (0.14), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 956 TYR 0.047 0.003 TYR E 408 PHE 0.035 0.003 PHE C 809 TRP 0.032 0.003 TRP E 434 HIS 0.018 0.002 HIS D 590 Details of bonding type rmsd covalent geometry : bond 0.00695 (31638) covalent geometry : angle 0.84646 (42956) hydrogen bonds : bond 0.05252 ( 1879) hydrogen bonds : angle 5.14050 ( 5430) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 456 time to evaluate : 1.047 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: B 266 LEU cc_start: 0.6970 (mt) cc_final: 0.6717 (mt) REVERT: B 402 MET cc_start: 0.4391 (OUTLIER) cc_final: 0.2535 (mtm) REVERT: B 503 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.5649 (tm-30) REVERT: B 615 GLU cc_start: 0.4881 (OUTLIER) cc_final: 0.4397 (pm20) REVERT: B 628 TRP cc_start: 0.6243 (OUTLIER) cc_final: 0.5156 (m100) REVERT: C 240 ARG cc_start: 0.7112 (mmm-85) cc_final: 0.6878 (tpp80) REVERT: C 243 MET cc_start: 0.7070 (mmm) cc_final: 0.6353 (tpp) REVERT: C 455 MET cc_start: 0.5664 (ppp) cc_final: 0.5022 (ppp) REVERT: C 623 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7575 (t80) REVERT: C 728 ASP cc_start: 0.5706 (t70) cc_final: 0.5444 (t70) REVERT: C 857 ARG cc_start: 0.5797 (ttt-90) cc_final: 0.4792 (mmm-85) REVERT: C 1015 LYS cc_start: 0.7818 (mmtm) cc_final: 0.7361 (mtmt) REVERT: C 1072 LEU cc_start: 0.8844 (mm) cc_final: 0.8507 (pp) REVERT: D 480 MET cc_start: 0.6593 (ppp) cc_final: 0.5733 (tmm) REVERT: D 481 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7357 (m-30) REVERT: E 207 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7438 (p0) REVERT: E 223 LYS cc_start: 0.5627 (mptt) cc_final: 0.4428 (ttmt) REVERT: E 227 LYS cc_start: 0.6748 (tptm) cc_final: 0.5961 (pptt) REVERT: E 280 CYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6785 (p) REVERT: E 391 GLU cc_start: 0.5849 (tt0) cc_final: 0.4282 (pm20) REVERT: E 431 MET cc_start: 0.5177 (mmp) cc_final: 0.4132 (ttt) REVERT: E 437 TYR cc_start: 0.6549 (OUTLIER) cc_final: 0.5050 (p90) REVERT: G 39 ASP cc_start: 0.6473 (t0) cc_final: 0.6264 (t0) REVERT: G 41 LYS cc_start: 0.8538 (mppt) cc_final: 0.8329 (mppt) REVERT: G 151 TYR cc_start: 0.5523 (m-10) cc_final: 0.4958 (m-80) REVERT: G 155 ARG cc_start: 0.7766 (mtp-110) cc_final: 0.7029 (mmt90) REVERT: I 64 ASP cc_start: 0.7444 (t0) cc_final: 0.6702 (t70) REVERT: I 76 SER cc_start: 0.8750 (p) cc_final: 0.8456 (m) REVERT: I 94 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.7747 (p90) REVERT: J 39 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.6931 (ppp) REVERT: J 45 ASP cc_start: 0.8227 (p0) cc_final: 0.7771 (p0) REVERT: J 64 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7537 (mt0) REVERT: K 47 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6726 (tm-30) REVERT: K 67 TYR cc_start: 0.5222 (OUTLIER) cc_final: 0.3500 (t80) REVERT: L 38 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7582 (tttt) REVERT: L 48 PHE cc_start: 0.6456 (OUTLIER) cc_final: 0.6203 (t80) REVERT: L 62 ARG cc_start: 0.5285 (mtt-85) cc_final: 0.4886 (mtm-85) REVERT: L 82 GLN cc_start: 0.6597 (tp-100) cc_final: 0.5098 (mm110) REVERT: M 15 MET cc_start: 0.6061 (ppp) cc_final: 0.5746 (ppp) REVERT: M 19 MET cc_start: 0.6533 (ptm) cc_final: 0.5869 (tmm) REVERT: M 45 LYS cc_start: 0.6701 (OUTLIER) cc_final: 0.6444 (tptm) REVERT: P 21 VAL cc_start: 0.7539 (OUTLIER) cc_final: 0.7300 (m) REVERT: P 53 THR cc_start: 0.8173 (p) cc_final: 0.7920 (t) REVERT: P 79 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6809 (tm-30) REVERT: P 95 ARG cc_start: 0.6779 (ttm110) cc_final: 0.6555 (ttm110) outliers start: 147 outliers final: 104 residues processed: 560 average time/residue: 0.1920 time to fit residues: 172.2570 Evaluate side-chains 570 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 449 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 TRP Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 690 PHE Chi-restraints excluded: chain B residue 816 LYS Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 773 THR Chi-restraints excluded: chain C residue 846 VAL Chi-restraints excluded: chain C residue 925 CYS Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1010 PHE Chi-restraints excluded: chain C residue 1041 HIS Chi-restraints excluded: chain D residue 258 HIS Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 325 PHE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 413 TRP Chi-restraints excluded: chain D residue 481 ASP Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 555 LYS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 590 HIS Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 291 TRP Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 340 ILE Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 414 TRP Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 437 TYR Chi-restraints excluded: chain E residue 450 SER Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 476 SER Chi-restraints excluded: chain E residue 495 ILE Chi-restraints excluded: chain E residue 503 THR Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 94 TYR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 39 MET Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain K residue 67 TYR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain L residue 38 LYS Chi-restraints excluded: chain L residue 48 PHE Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 67 TYR Chi-restraints excluded: chain L residue 79 TYR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain P residue 9 MET Chi-restraints excluded: chain P residue 19 THR Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Z residue 73 LEU Chi-restraints excluded: chain Z residue 158 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 334 optimal weight: 4.9990 chunk 250 optimal weight: 0.7980 chunk 419 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 264 optimal weight: 0.9980 chunk 430 optimal weight: 6.9990 chunk 378 optimal weight: 40.0000 chunk 339 optimal weight: 6.9990 chunk 228 optimal weight: 0.0050 chunk 270 optimal weight: 0.7980 chunk 251 optimal weight: 0.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 392 GLN C 515 HIS D 270 ASN ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 GLN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 76 GLN ** Z 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.130523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.120660 restraints weight = 74716.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.120785 restraints weight = 148966.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.119625 restraints weight = 85568.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.119212 restraints weight = 98768.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.119248 restraints weight = 85287.627| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31638 Z= 0.137 Angle : 0.694 16.331 42956 Z= 0.357 Chirality : 0.043 0.176 5051 Planarity : 0.005 0.070 5639 Dihedral : 5.662 86.153 4592 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.22 % Favored : 93.75 % Rotamer: Outliers : 3.82 % Allowed : 26.44 % Favored : 69.74 % 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: -1.61 (0.13), residues: 3985 helix: 0.67 (0.12), residues: 1908 sheet: -2.05 (0.23), residues: 495 loop : -3.01 (0.14), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 217 TYR 0.021 0.002 TYR P 78 PHE 0.046 0.002 PHE C 809 TRP 0.032 0.002 TRP B 589 HIS 0.009 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00291 (31638) covalent geometry : angle 0.69399 (42956) hydrogen bonds : bond 0.04325 ( 1879) hydrogen bonds : angle 4.68038 ( 5430) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 475 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 266 LEU cc_start: 0.6720 (mt) cc_final: 0.6407 (mt) REVERT: B 402 MET cc_start: 0.4764 (OUTLIER) cc_final: 0.2460 (mtp) REVERT: B 628 TRP cc_start: 0.5919 (OUTLIER) cc_final: 0.5009 (m100) REVERT: B 798 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.6805 (pt) REVERT: C 140 MET cc_start: 0.5396 (tpt) cc_final: 0.2646 (pmm) REVERT: C 240 ARG cc_start: 0.6865 (mmm-85) cc_final: 0.6489 (tpp80) REVERT: C 243 MET cc_start: 0.6697 (mmm) cc_final: 0.6319 (mmm) REVERT: C 455 MET cc_start: 0.5760 (ppp) cc_final: 0.5007 (ppp) REVERT: C 491 GLN cc_start: 0.6718 (OUTLIER) cc_final: 0.6492 (pm20) REVERT: C 605 GLU cc_start: 0.5092 (pm20) cc_final: 0.4567 (pm20) REVERT: C 623 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7625 (t80) REVERT: C 767 ARG cc_start: 0.5208 (ppt170) cc_final: 0.4711 (ttp80) REVERT: C 857 ARG cc_start: 0.5248 (ttt-90) cc_final: 0.4403 (mmm-85) REVERT: C 1015 LYS cc_start: 0.7552 (mmtm) cc_final: 0.7149 (mtmt) REVERT: D 481 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7514 (m-30) REVERT: D 535 MET cc_start: 0.7073 (mmt) cc_final: 0.6689 (mmp) REVERT: D 598 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7667 (mmtm) REVERT: D 663 LEU cc_start: 0.8682 (tp) cc_final: 0.8451 (tp) REVERT: E 223 LYS cc_start: 0.5449 (mptt) cc_final: 0.4447 (ttmt) REVERT: E 227 LYS cc_start: 0.6458 (tptm) cc_final: 0.5447 (pptt) REVERT: E 391 GLU cc_start: 0.5610 (tt0) cc_final: 0.4228 (pm20) REVERT: E 431 MET cc_start: 0.4840 (mmp) cc_final: 0.4049 (ttt) REVERT: E 437 TYR cc_start: 0.6273 (OUTLIER) cc_final: 0.5449 (p90) REVERT: G 103 PHE cc_start: 0.6351 (t80) cc_final: 0.5670 (t80) REVERT: G 151 TYR cc_start: 0.5600 (m-10) cc_final: 0.5066 (m-80) REVERT: G 155 ARG cc_start: 0.7590 (mtp-110) cc_final: 0.7089 (mmt90) REVERT: I 94 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.7564 (p90) REVERT: J 39 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.6445 (ppp) REVERT: J 45 ASP cc_start: 0.8096 (p0) cc_final: 0.7667 (p0) REVERT: J 64 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7349 (mt0) REVERT: K 47 GLU cc_start: 0.7009 (tm-30) cc_final: 0.6780 (tm-30) REVERT: K 67 TYR cc_start: 0.4995 (OUTLIER) cc_final: 0.3902 (t80) REVERT: L 48 PHE cc_start: 0.6670 (OUTLIER) cc_final: 0.6457 (t80) REVERT: L 82 GLN cc_start: 0.6545 (tp-100) cc_final: 0.5108 (mm110) REVERT: M 15 MET cc_start: 0.6151 (ppp) cc_final: 0.5848 (ppp) REVERT: M 19 MET cc_start: 0.5855 (ptm) cc_final: 0.5120 (tmm) REVERT: M 45 LYS cc_start: 0.6238 (OUTLIER) cc_final: 0.6010 (tttp) REVERT: P 21 VAL cc_start: 0.7615 (OUTLIER) cc_final: 0.7390 (m) REVERT: P 53 THR cc_start: 0.8071 (p) cc_final: 0.7781 (t) REVERT: P 95 ARG cc_start: 0.6788 (ttm110) cc_final: 0.6495 (ttm110) REVERT: Z 58 MET cc_start: 0.2335 (pmm) cc_final: 0.1559 (ppp) outliers start: 103 outliers final: 64 residues processed: 538 average time/residue: 0.1916 time to fit residues: 167.0220 Evaluate side-chains 537 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 458 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 TRP Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 690 PHE Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 816 LYS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 488 PHE Chi-restraints excluded: chain C residue 491 GLN Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 846 VAL Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1010 PHE Chi-restraints excluded: chain C residue 1041 HIS Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 258 HIS Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 481 ASP Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 590 HIS Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 291 TRP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 414 TRP Chi-restraints excluded: chain E residue 437 TYR Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 94 TYR Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 39 MET Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain K residue 67 TYR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain L residue 48 PHE Chi-restraints excluded: chain L residue 79 TYR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain P residue 9 MET Chi-restraints excluded: chain P residue 19 THR Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain Z residue 73 LEU Chi-restraints excluded: chain Z residue 158 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 293 optimal weight: 30.0000 chunk 359 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 16 optimal weight: 50.0000 chunk 61 optimal weight: 5.9990 chunk 291 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 515 HIS C 869 GLN D 270 ASN ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.121123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.103512 restraints weight = 76456.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.104203 restraints weight = 133480.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.105199 restraints weight = 87253.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.105209 restraints weight = 59249.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.105772 restraints weight = 49887.519| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.118 31638 Z= 0.318 Angle : 0.874 22.181 42956 Z= 0.457 Chirality : 0.051 0.239 5051 Planarity : 0.006 0.071 5639 Dihedral : 6.138 54.372 4589 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.02 % Favored : 88.93 % Rotamer: Outliers : 4.72 % Allowed : 25.73 % Favored : 69.55 % 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: -2.03 (0.13), residues: 3985 helix: 0.31 (0.11), residues: 1907 sheet: -2.15 (0.23), residues: 511 loop : -3.22 (0.14), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 217 TYR 0.043 0.003 TYR E 408 PHE 0.052 0.003 PHE C 809 TRP 0.032 0.003 TRP E 434 HIS 0.018 0.002 HIS D 590 Details of bonding type rmsd covalent geometry : bond 0.00723 (31638) covalent geometry : angle 0.87438 (42956) hydrogen bonds : bond 0.05297 ( 1879) hydrogen bonds : angle 5.15830 ( 5430) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 456 time to evaluate : 1.127 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: B 266 LEU cc_start: 0.7027 (mt) cc_final: 0.6701 (mt) REVERT: B 402 MET cc_start: 0.4229 (OUTLIER) cc_final: 0.2499 (mtp) REVERT: B 628 TRP cc_start: 0.6003 (OUTLIER) cc_final: 0.4976 (m100) REVERT: C 140 MET cc_start: 0.5216 (tpt) cc_final: 0.2305 (pmm) REVERT: C 200 LEU cc_start: 0.5465 (OUTLIER) cc_final: 0.5111 (pp) REVERT: C 240 ARG cc_start: 0.7280 (mmm-85) cc_final: 0.7037 (tpp80) REVERT: C 243 MET cc_start: 0.7108 (mmm) cc_final: 0.6420 (tpp) REVERT: C 455 MET cc_start: 0.5329 (ppp) cc_final: 0.4719 (ppp) REVERT: C 623 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7604 (t80) REVERT: C 857 ARG cc_start: 0.5857 (ttt-90) cc_final: 0.4768 (mmm-85) REVERT: C 1015 LYS cc_start: 0.7911 (mmtm) cc_final: 0.7426 (mtmt) REVERT: D 217 ARG cc_start: 0.6622 (mtm-85) cc_final: 0.5911 (ttt-90) REVERT: D 480 MET cc_start: 0.6723 (ppp) cc_final: 0.5862 (tmm) REVERT: D 481 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7398 (m-30) REVERT: D 558 VAL cc_start: 0.8921 (OUTLIER) cc_final: 0.8543 (t) REVERT: E 223 LYS cc_start: 0.5354 (mptt) cc_final: 0.4197 (ttmt) REVERT: E 227 LYS cc_start: 0.6888 (tptm) cc_final: 0.5935 (pptt) REVERT: E 391 GLU cc_start: 0.5890 (tt0) cc_final: 0.4284 (pm20) REVERT: E 431 MET cc_start: 0.5130 (mmp) cc_final: 0.4071 (ttt) REVERT: E 437 TYR cc_start: 0.6642 (OUTLIER) cc_final: 0.5207 (p90) REVERT: G 103 PHE cc_start: 0.6977 (t80) cc_final: 0.6172 (t80) REVERT: G 151 TYR cc_start: 0.5428 (m-10) cc_final: 0.4907 (m-80) REVERT: G 155 ARG cc_start: 0.7863 (mtp-110) cc_final: 0.7049 (mmt90) REVERT: I 64 ASP cc_start: 0.7322 (t0) cc_final: 0.6723 (t0) REVERT: I 76 SER cc_start: 0.8792 (p) cc_final: 0.8512 (m) REVERT: I 94 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7759 (p90) REVERT: J 39 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.6955 (ppp) REVERT: J 45 ASP cc_start: 0.8198 (p0) cc_final: 0.7783 (p0) REVERT: J 64 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7512 (mt0) REVERT: K 47 GLU cc_start: 0.7351 (tm-30) cc_final: 0.6817 (tm-30) REVERT: K 67 TYR cc_start: 0.5052 (OUTLIER) cc_final: 0.3251 (t80) REVERT: L 38 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7546 (tttt) REVERT: L 48 PHE cc_start: 0.6501 (OUTLIER) cc_final: 0.6203 (t80) REVERT: L 62 ARG cc_start: 0.5801 (mtm-85) cc_final: 0.5273 (mtm-85) REVERT: L 82 GLN cc_start: 0.6930 (tp-100) cc_final: 0.5471 (mm110) REVERT: M 15 MET cc_start: 0.6412 (ppp) cc_final: 0.6210 (ppp) REVERT: M 20 GLN cc_start: 0.7259 (tp40) cc_final: 0.7046 (tp40) REVERT: M 45 LYS cc_start: 0.6759 (OUTLIER) cc_final: 0.6486 (tptm) REVERT: P 21 VAL cc_start: 0.7543 (OUTLIER) cc_final: 0.7282 (m) REVERT: P 54 GLN cc_start: 0.8074 (tp40) cc_final: 0.7732 (tp40) REVERT: P 95 ARG cc_start: 0.6750 (ttm110) cc_final: 0.6486 (ttm110) REVERT: P 100 LEU cc_start: 0.8146 (tp) cc_final: 0.7917 (tt) outliers start: 127 outliers final: 91 residues processed: 542 average time/residue: 0.1837 time to fit residues: 158.8830 Evaluate side-chains 553 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 447 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 TRP Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 690 PHE Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 816 LYS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 773 THR Chi-restraints excluded: chain C residue 846 VAL Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1010 PHE Chi-restraints excluded: chain C residue 1041 HIS Chi-restraints excluded: chain D residue 258 HIS Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 413 TRP Chi-restraints excluded: chain D residue 481 ASP Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 590 HIS Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 614 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain E residue 291 TRP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 414 TRP Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 437 TYR Chi-restraints excluded: chain E residue 450 SER Chi-restraints excluded: chain E residue 495 ILE Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 94 TYR Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 39 MET Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain K residue 67 TYR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain L residue 38 LYS Chi-restraints excluded: chain L residue 48 PHE Chi-restraints excluded: chain L residue 67 TYR Chi-restraints excluded: chain L residue 79 TYR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain P residue 9 MET Chi-restraints excluded: chain P residue 19 THR Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Z residue 73 LEU Chi-restraints excluded: chain Z residue 158 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 188 optimal weight: 8.9990 chunk 271 optimal weight: 0.5980 chunk 217 optimal weight: 0.9990 chunk 96 optimal weight: 30.0000 chunk 311 optimal weight: 20.0000 chunk 221 optimal weight: 0.8980 chunk 396 optimal weight: 20.0000 chunk 320 optimal weight: 4.9990 chunk 1 optimal weight: 50.0000 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 20.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 515 HIS D 270 ASN ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.123163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.106591 restraints weight = 75698.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.107683 restraints weight = 140941.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.108355 restraints weight = 77761.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.108580 restraints weight = 50812.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.108869 restraints weight = 44757.638| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 31638 Z= 0.197 Angle : 0.771 19.272 42956 Z= 0.398 Chirality : 0.046 0.218 5051 Planarity : 0.005 0.072 5639 Dihedral : 5.868 56.311 4589 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.21 % Favored : 91.77 % Rotamer: Outliers : 3.82 % Allowed : 27.07 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.13), residues: 3985 helix: 0.47 (0.12), residues: 1913 sheet: -2.07 (0.23), residues: 504 loop : -3.13 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 217 TYR 0.034 0.002 TYR E 199 PHE 0.037 0.002 PHE C 809 TRP 0.035 0.003 TRP E 271 HIS 0.010 0.001 HIS D 590 Details of bonding type rmsd covalent geometry : bond 0.00447 (31638) covalent geometry : angle 0.77128 (42956) hydrogen bonds : bond 0.04773 ( 1879) hydrogen bonds : angle 4.90891 ( 5430) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7970 Ramachandran restraints generated. 3985 Oldfield, 0 Emsley, 3985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 457 time to evaluate : 0.980 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: B 266 LEU cc_start: 0.6979 (mt) cc_final: 0.6659 (mt) REVERT: B 402 MET cc_start: 0.4587 (OUTLIER) cc_final: 0.2391 (mtp) REVERT: B 628 TRP cc_start: 0.6029 (OUTLIER) cc_final: 0.5024 (m100) REVERT: C 140 MET cc_start: 0.5045 (tpt) cc_final: 0.2370 (pmm) REVERT: C 200 LEU cc_start: 0.5625 (OUTLIER) cc_final: 0.5406 (tm) REVERT: C 240 ARG cc_start: 0.7230 (mmm-85) cc_final: 0.6976 (tpp80) REVERT: C 243 MET cc_start: 0.7049 (mmm) cc_final: 0.6305 (tpp) REVERT: C 348 LYS cc_start: 0.7117 (ptpt) cc_final: 0.6873 (ttpt) REVERT: C 455 MET cc_start: 0.5150 (ppp) cc_final: 0.4135 (ppp) REVERT: C 623 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7509 (t80) REVERT: C 730 MET cc_start: 0.6888 (tpp) cc_final: 0.6597 (tpp) REVERT: C 857 ARG cc_start: 0.5684 (ttt-90) cc_final: 0.4624 (mmm-85) REVERT: C 1015 LYS cc_start: 0.7873 (mmtm) cc_final: 0.7387 (mtmt) REVERT: D 480 MET cc_start: 0.6544 (ppp) cc_final: 0.5941 (ppp) REVERT: D 481 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7398 (m-30) REVERT: D 535 MET cc_start: 0.7313 (mmp) cc_final: 0.6882 (mmp) REVERT: E 223 LYS cc_start: 0.5017 (mptt) cc_final: 0.3894 (ttmt) REVERT: E 431 MET cc_start: 0.5117 (mmp) cc_final: 0.3922 (ttt) REVERT: E 437 TYR cc_start: 0.6314 (OUTLIER) cc_final: 0.4972 (p90) REVERT: G 39 ASP cc_start: 0.6591 (t0) cc_final: 0.6374 (t0) REVERT: G 41 LYS cc_start: 0.8499 (mppt) cc_final: 0.8241 (mppt) REVERT: G 103 PHE cc_start: 0.6908 (t80) cc_final: 0.6021 (t80) REVERT: G 151 TYR cc_start: 0.5632 (m-10) cc_final: 0.5398 (m-80) REVERT: I 64 ASP cc_start: 0.7464 (t0) cc_final: 0.6767 (t0) REVERT: I 76 SER cc_start: 0.8738 (p) cc_final: 0.8424 (m) REVERT: I 94 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7538 (p90) REVERT: J 39 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.6868 (ppp) REVERT: J 45 ASP cc_start: 0.8111 (p0) cc_final: 0.7852 (p0) REVERT: J 64 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7401 (mt0) REVERT: K 47 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6857 (tm-30) REVERT: L 38 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7561 (tttt) REVERT: L 48 PHE cc_start: 0.6470 (OUTLIER) cc_final: 0.6155 (t80) REVERT: L 82 GLN cc_start: 0.6822 (tp-100) cc_final: 0.5429 (mm110) REVERT: M 15 MET cc_start: 0.6084 (ppp) cc_final: 0.5809 (ppp) REVERT: M 20 GLN cc_start: 0.7102 (tp40) cc_final: 0.6823 (tp40) REVERT: M 45 LYS cc_start: 0.6590 (OUTLIER) cc_final: 0.6389 (tptm) REVERT: P 21 VAL cc_start: 0.7067 (OUTLIER) cc_final: 0.6815 (m) REVERT: P 95 ARG cc_start: 0.6847 (ttm110) cc_final: 0.6544 (ttm110) REVERT: Z 12 ARG cc_start: 0.7680 (tpt170) cc_final: 0.7311 (tpt90) REVERT: Z 83 ARG cc_start: 0.4400 (mpp-170) cc_final: 0.3788 (mtm-85) outliers start: 103 outliers final: 83 residues processed: 524 average time/residue: 0.1857 time to fit residues: 155.1847 Evaluate side-chains 547 residues out of total 3603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 451 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 TRP Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 690 PHE Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 816 LYS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 491 GLN Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 552 ASP Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 838 TYR Chi-restraints excluded: chain C residue 846 VAL Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 1010 PHE Chi-restraints excluded: chain C residue 1041 HIS Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 258 HIS Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 413 TRP Chi-restraints excluded: chain D residue 481 ASP Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 590 HIS Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 291 TRP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 414 TRP Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 437 TYR Chi-restraints excluded: chain E residue 495 ILE Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 94 TYR Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 39 MET Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain L residue 38 LYS Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 48 PHE Chi-restraints excluded: chain L residue 79 TYR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain P residue 9 MET Chi-restraints excluded: chain P residue 19 THR Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Z residue 73 LEU Chi-restraints excluded: chain Z residue 158 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 216 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 240 optimal weight: 30.0000 chunk 105 optimal weight: 50.0000 chunk 273 optimal weight: 0.3980 chunk 204 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 387 optimal weight: 1.9990 chunk 354 optimal weight: 0.0030 chunk 388 optimal weight: 20.0000 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 515 HIS C 545 GLN D 270 ASN E 125 ASN ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 HIS ** M 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 155 HIS ** 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 = 0.4188 r_free = 0.4188 target = 0.129626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.114312 restraints weight = 76020.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.115061 restraints weight = 148718.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.115934 restraints weight = 91940.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.115797 restraints weight = 71954.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.117447 restraints weight = 52143.575| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31638 Z= 0.130 Angle : 0.695 14.740 42956 Z= 0.353 Chirality : 0.043 0.209 5051 Planarity : 0.004 0.073 5639 Dihedral : 5.155 58.849 4589 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.27 % Favored : 93.70 % Rotamer: Outliers : 3.27 % Allowed : 27.70 % Favored : 69.03 % 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: -1.31 (0.13), residues: 3985 helix: 0.92 (0.12), residues: 1911 sheet: -1.93 (0.22), residues: 521 loop : -2.85 (0.14), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 217 TYR 0.024 0.002 TYR K 79 PHE 0.035 0.002 PHE C 809 TRP 0.038 0.002 TRP B 589 HIS 0.008 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00279 (31638) covalent geometry : angle 0.69505 (42956) hydrogen bonds : bond 0.03968 ( 1879) hydrogen bonds : angle 4.52067 ( 5430) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6823.05 seconds wall clock time: 117 minutes 47.74 seconds (7067.74 seconds total)