Starting phenix.real_space_refine on Thu Jun 19 10:57:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tys_26193/06_2025/7tys_26193.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tys_26193/06_2025/7tys_26193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tys_26193/06_2025/7tys_26193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tys_26193/06_2025/7tys_26193.map" model { file = "/net/cci-nas-00/data/ceres_data/7tys_26193/06_2025/7tys_26193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tys_26193/06_2025/7tys_26193.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 P 32 5.49 5 S 109 5.16 5 C 13777 2.51 5 N 3588 2.21 5 O 3778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21286 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2660 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 16, 'TRANS': 344} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 14, 'ARG:plan': 8, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 125 Chain: "B" Number of atoms: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2531 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 13, 'TRANS': 319} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 61 Chain: "C" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2515 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 13, 'TRANS': 318} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "D" Number of atoms: 2511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2511 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 317} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 62 Chain: "E" Number of atoms: 10155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1431, 10155 Classifications: {'peptide': 1431} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 335} Link IDs: {'PTRANS': 48, 'TRANS': 1382} Chain breaks: 4 Unresolved non-hydrogen bonds: 1180 Unresolved non-hydrogen angles: 1469 Unresolved non-hydrogen dihedrals: 954 Unresolved non-hydrogen chiralities: 112 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 30, 'PHE:plan': 16, 'GLU:plan': 37, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 620 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 177 Unusual residues: {' K': 2, 'ATP': 1, 'POV': 1} Classifications: {'peptide': 2, 'undetermined': 4} Link IDs: {'TRANS': 1, None: 4} Not linked: pdbres="ATP A 401 " pdbres=" K A 402 " Not linked: pdbres=" K A 402 " pdbres=" K A 403 " Not linked: pdbres=" K A 403 " pdbres="POV A 404 " Not linked: pdbres="POV A 404 " pdbres="P5S A 405 " Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'ATP': 1, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'ATP': 1, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'ATP': 1, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 346 Unusual residues: {'65I': 6, 'ATP': 1, 'BJX': 1, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 9} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 12.58, per 1000 atoms: 0.59 Number of scatterers: 21286 At special positions: 0 Unit cell: (165.11, 107.635, 145.255, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 109 16.00 P 32 15.00 O 3778 8.00 N 3588 7.00 C 13777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 26 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG F 1 " - " ASN E 10 " Time building additional restraints: 5.69 Conformation dependent library (CDL) restraints added in 2.6 seconds 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5266 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 37 sheets defined 53.0% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 removed outlier: 4.223A pdb=" N THR A 28 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 29 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 30 " --> pdb=" O ARG A 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 25 through 30' Processing helix chain 'A' and resid 53 through 58 removed outlier: 3.929A pdb=" N ASP A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 66 removed outlier: 3.663A pdb=" N VAL A 64 " --> pdb=" O PHE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 98 removed outlier: 3.569A pdb=" N SER A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 129 Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.693A pdb=" N LEU A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'B' and resid 53 through 58 removed outlier: 3.772A pdb=" N ASP B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 66 Processing helix chain 'B' and resid 67 through 97 removed outlier: 3.503A pdb=" N LEU B 73 " --> pdb=" O PRO B 69 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 130 Processing helix chain 'B' and resid 142 through 172 removed outlier: 3.781A pdb=" N ILE B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 265 through 270 removed outlier: 4.276A pdb=" N ASP B 269 " --> pdb=" O PRO B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 345 through 362 Processing helix chain 'C' and resid 53 through 58 Processing helix chain 'C' and resid 58 through 66 Processing helix chain 'C' and resid 67 through 97 removed outlier: 3.593A pdb=" N LEU C 73 " --> pdb=" O PRO C 69 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 129 Processing helix chain 'C' and resid 142 through 172 removed outlier: 3.747A pdb=" N ILE C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 265 through 270 removed outlier: 4.509A pdb=" N ASP C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.542A pdb=" N LEU C 275 " --> pdb=" O PRO C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 333 No H-bonds generated for 'chain 'C' and resid 331 through 333' Processing helix chain 'C' and resid 345 through 361 Processing helix chain 'D' and resid 53 through 58 removed outlier: 3.824A pdb=" N ASP D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 67 through 98 removed outlier: 3.638A pdb=" N GLY D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 129 Processing helix chain 'D' and resid 142 through 172 removed outlier: 3.799A pdb=" N ILE D 146 " --> pdb=" O CYS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 removed outlier: 3.536A pdb=" N ALA D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU D 179 " --> pdb=" O HIS D 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 174 through 179' Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 345 through 360 Processing helix chain 'E' and resid 8 through 13 removed outlier: 3.880A pdb=" N ALA E 13 " --> pdb=" O GLU E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 24 Processing helix chain 'E' and resid 26 through 32 Processing helix chain 'E' and resid 33 through 55 removed outlier: 3.614A pdb=" N LEU E 39 " --> pdb=" O PRO E 35 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE E 44 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 56 through 57 No H-bonds generated for 'chain 'E' and resid 56 through 57' Processing helix chain 'E' and resid 58 through 62 removed outlier: 3.621A pdb=" N HIS E 62 " --> pdb=" O HIS E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 96 Processing helix chain 'E' and resid 107 through 130 removed outlier: 3.603A pdb=" N SER E 130 " --> pdb=" O ASN E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 134 No H-bonds generated for 'chain 'E' and resid 132 through 134' Processing helix chain 'E' and resid 135 through 160 removed outlier: 3.873A pdb=" N LEU E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 194 Processing helix chain 'E' and resid 207 through 212 removed outlier: 3.638A pdb=" N ASP E 212 " --> pdb=" O GLU E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 230 Processing helix chain 'E' and resid 232 through 243 removed outlier: 4.269A pdb=" N PHE E 236 " --> pdb=" O TRP E 232 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS E 241 " --> pdb=" O ILE E 237 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS E 242 " --> pdb=" O LYS E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 257 Processing helix chain 'E' and resid 258 through 277 Processing helix chain 'E' and resid 283 through 314 removed outlier: 5.310A pdb=" N ARG E 297 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU E 301 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE E 314 " --> pdb=" O ASP E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 328 Processing helix chain 'E' and resid 347 through 352 Processing helix chain 'E' and resid 354 through 401 removed outlier: 3.765A pdb=" N GLN E 374 " --> pdb=" O ARG E 370 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR E 393 " --> pdb=" O GLY E 389 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 413 through 456 removed outlier: 3.614A pdb=" N VAL E 421 " --> pdb=" O ILE E 417 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR E 425 " --> pdb=" O VAL E 421 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Proline residue: E 436 - end of helix removed outlier: 3.799A pdb=" N TRP E 439 " --> pdb=" O CYS E 435 " (cutoff:3.500A) Proline residue: E 442 - end of helix removed outlier: 3.676A pdb=" N TYR E 454 " --> pdb=" O ILE E 450 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU E 456 " --> pdb=" O LEU E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 505 removed outlier: 3.731A pdb=" N VAL E 466 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE E 467 " --> pdb=" O GLY E 463 " (cutoff:3.500A) Proline residue: E 472 - end of helix removed outlier: 3.507A pdb=" N GLU E 501 " --> pdb=" O LYS E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 512 removed outlier: 3.537A pdb=" N TYR E 512 " --> pdb=" O LEU E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 565 removed outlier: 3.593A pdb=" N SER E 520 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG E 521 " --> pdb=" O ILE E 517 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL E 522 " --> pdb=" O PHE E 518 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER E 532 " --> pdb=" O LYS E 528 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE E 550 " --> pdb=" O MET E 546 " (cutoff:3.500A) Proline residue: E 551 - end of helix Processing helix chain 'E' and resid 572 through 591 removed outlier: 3.766A pdb=" N ALA E 578 " --> pdb=" O SER E 574 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER E 581 " --> pdb=" O PHE E 577 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR E 588 " --> pdb=" O HIS E 584 " (cutoff:3.500A) Proline residue: E 589 - end of helix Processing helix chain 'E' and resid 592 through 615 removed outlier: 3.563A pdb=" N SER E 615 " --> pdb=" O SER E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 719 through 726 Processing helix chain 'E' and resid 784 through 790 Processing helix chain 'E' and resid 795 through 807 removed outlier: 3.585A pdb=" N MET E 801 " --> pdb=" O GLN E 797 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL E 802 " --> pdb=" O ARG E 798 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA E 805 " --> pdb=" O MET E 801 " (cutoff:3.500A) Processing helix chain 'E' and resid 808 through 813 Processing helix chain 'E' and resid 817 through 820 Processing helix chain 'E' and resid 831 through 846 removed outlier: 3.615A pdb=" N LEU E 844 " --> pdb=" O VAL E 840 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN E 846 " --> pdb=" O ARG E 842 " (cutoff:3.500A) Processing helix chain 'E' and resid 862 through 880 removed outlier: 3.528A pdb=" N HIS E 867 " --> pdb=" O HIS E 863 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU E 868 " --> pdb=" O LEU E 864 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET E 869 " --> pdb=" O SER E 865 " (cutoff:3.500A) Processing helix chain 'E' and resid 914 through 919 removed outlier: 4.324A pdb=" N GLN E 918 " --> pdb=" O LEU E 914 " (cutoff:3.500A) Processing helix chain 'E' and resid 988 through 993 Processing helix chain 'E' and resid 997 through 1008 removed outlier: 3.614A pdb=" N CYS E1001 " --> pdb=" O PRO E 997 " (cutoff:3.500A) Processing helix chain 'E' and resid 1010 through 1042 removed outlier: 3.597A pdb=" N ASP E1031 " --> pdb=" O LEU E1027 " (cutoff:3.500A) Processing helix chain 'E' and resid 1066 through 1106 Processing helix chain 'E' and resid 1109 through 1116 removed outlier: 3.941A pdb=" N PHE E1113 " --> pdb=" O PRO E1109 " (cutoff:3.500A) Processing helix chain 'E' and resid 1119 through 1135 removed outlier: 5.015A pdb=" N ASP E1128 " --> pdb=" O ARG E1124 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1135 through 1161 removed outlier: 4.111A pdb=" N GLU E1141 " --> pdb=" O PRO E1137 " (cutoff:3.500A) Processing helix chain 'E' and resid 1163 through 1210 removed outlier: 3.908A pdb=" N ALA E1167 " --> pdb=" O VAL E1163 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU E1169 " --> pdb=" O LEU E1165 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 3.687A pdb=" N VAL E1174 " --> pdb=" O PRO E1170 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG E1183 " --> pdb=" O GLN E1179 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL E1184 " --> pdb=" O LYS E1180 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP E1188 " --> pdb=" O VAL E1184 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN E1197 " --> pdb=" O ASP E1193 " (cutoff:3.500A) Proline residue: E1199 - end of helix Processing helix chain 'E' and resid 1210 through 1218 Processing helix chain 'E' and resid 1219 through 1271 removed outlier: 3.874A pdb=" N GLY E1256 " --> pdb=" O MET E1252 " (cutoff:3.500A) Processing helix chain 'E' and resid 1278 through 1287 removed outlier: 3.768A pdb=" N GLY E1282 " --> pdb=" O ALA E1278 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU E1283 " --> pdb=" O GLY E1279 " (cutoff:3.500A) Processing helix chain 'E' and resid 1290 through 1319 removed outlier: 3.576A pdb=" N ALA E1311 " --> pdb=" O ILE E1307 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) Processing helix chain 'E' and resid 1382 through 1393 removed outlier: 3.877A pdb=" N SER E1387 " --> pdb=" O SER E1383 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE E1388 " --> pdb=" O GLY E1384 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E1390 " --> pdb=" O SER E1386 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE E1393 " --> pdb=" O SER E1389 " (cutoff:3.500A) Processing helix chain 'E' and resid 1414 through 1421 removed outlier: 3.769A pdb=" N ARG E1421 " --> pdb=" O THR E1417 " (cutoff:3.500A) Processing helix chain 'E' and resid 1449 through 1459 removed outlier: 3.553A pdb=" N GLU E1456 " --> pdb=" O TRP E1452 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN E1459 " --> pdb=" O LEU E1455 " (cutoff:3.500A) Processing helix chain 'E' and resid 1460 through 1467 removed outlier: 3.629A pdb=" N LYS E1465 " --> pdb=" O LYS E1461 " (cutoff:3.500A) Processing helix chain 'E' and resid 1469 through 1473 removed outlier: 4.022A pdb=" N ASP E1472 " --> pdb=" O GLY E1469 " (cutoff:3.500A) Processing helix chain 'E' and resid 1485 through 1498 Processing helix chain 'E' and resid 1512 through 1529 removed outlier: 3.867A pdb=" N THR E1516 " --> pdb=" O ILE E1512 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU E1517 " --> pdb=" O ASP E1513 " (cutoff:3.500A) Processing helix chain 'E' and resid 1539 through 1545 removed outlier: 4.023A pdb=" N SER E1545 " --> pdb=" O HIS E1541 " (cutoff:3.500A) Processing helix chain 'E' and resid 1564 through 1570 removed outlier: 3.889A pdb=" N SER E1568 " --> pdb=" O GLU E1564 " (cutoff:3.500A) Processing helix chain 'E' and resid 1570 through 1578 removed outlier: 3.765A pdb=" N PHE E1574 " --> pdb=" O LYS E1570 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 removed outlier: 3.562A pdb=" N GLY A 40 " --> pdb=" O SER A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA4, first strand: chain 'A' and resid 259 through 260 removed outlier: 6.706A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 231 through 238 removed outlier: 4.927A pdb=" N THR A 223 " --> pdb=" O PRO A 232 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA A 213 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 231 through 238 removed outlier: 4.927A pdb=" N THR A 223 " --> pdb=" O PRO A 232 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N SER A 212 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL A 290 " --> pdb=" O SER A 212 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 289 " --> pdb=" O THR A 298 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 313 through 315 Processing sheet with id=AA8, first strand: chain 'A' and resid 326 through 329 removed outlier: 3.605A pdb=" N ALA D 45 " --> pdb=" O TYR A 326 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 36 through 37 Processing sheet with id=AB1, first strand: chain 'B' and resid 44 through 47 Processing sheet with id=AB2, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB3, first strand: chain 'B' and resid 195 through 199 removed outlier: 6.895A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 230 through 238 removed outlier: 5.242A pdb=" N THR B 223 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA B 213 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 249 " --> pdb=" O ALA B 213 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 230 through 238 removed outlier: 5.242A pdb=" N THR B 223 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N SER B 212 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL B 290 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 313 through 315 Processing sheet with id=AB7, first strand: chain 'C' and resid 36 through 37 Processing sheet with id=AB8, first strand: chain 'C' and resid 44 through 47 Processing sheet with id=AB9, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC1, first strand: chain 'C' and resid 259 through 260 removed outlier: 6.636A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 210 through 211 Processing sheet with id=AC3, first strand: chain 'C' and resid 230 through 238 removed outlier: 5.573A pdb=" N THR C 223 " --> pdb=" O PRO C 232 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 313 through 315 Processing sheet with id=AC5, first strand: chain 'D' and resid 36 through 37 Processing sheet with id=AC6, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AC7, first strand: chain 'D' and resid 259 through 260 removed outlier: 6.769A pdb=" N ALA D 187 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 230 through 238 removed outlier: 4.897A pdb=" N THR D 223 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N SER D 212 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL D 290 " --> pdb=" O SER D 212 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR D 214 " --> pdb=" O GLU D 288 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY D 289 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 313 through 315 Processing sheet with id=AD1, first strand: chain 'E' and resid 679 through 681 Processing sheet with id=AD2, first strand: chain 'E' and resid 686 through 687 Processing sheet with id=AD3, first strand: chain 'E' and resid 709 through 713 removed outlier: 3.536A pdb=" N ILE E 901 " --> pdb=" O MET E 710 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET E 903 " --> pdb=" O VAL E 712 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE E 900 " --> pdb=" O GLU E 911 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU E 911 " --> pdb=" O ILE E 900 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ALA E 902 " --> pdb=" O GLN E 909 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 782 through 783 removed outlier: 3.628A pdb=" N ALA E 782 " --> pdb=" O ILE E 823 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 850 through 854 removed outlier: 3.576A pdb=" N VAL E 887 " --> pdb=" O LEU E 853 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 1348 through 1351 removed outlier: 5.683A pdb=" N ASN E1349 " --> pdb=" O ARG E1402 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ARG E1402 " --> pdb=" O ASN E1349 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 1374 through 1376 removed outlier: 3.582A pdb=" N THR E1535 " --> pdb=" O ILE E1375 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 1404 through 1405 Processing sheet with id=AD9, first strand: chain 'E' and resid 1422 through 1424 removed outlier: 6.301A pdb=" N SER E1423 " --> pdb=" O ILE E1504 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'E' and resid 1549 through 1553 removed outlier: 7.363A pdb=" N VAL E1549 " --> pdb=" O PHE E1560 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE E1560 " --> pdb=" O VAL E1549 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL E1551 " --> pdb=" O LEU E1558 " (cutoff:3.500A) 1178 hydrogen bonds defined for protein. 3414 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.68 Time building geometry restraints manager: 6.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3536 1.32 - 1.45: 5521 1.45 - 1.57: 12437 1.57 - 1.69: 61 1.69 - 1.81: 170 Bond restraints: 21725 Sorted by residual: bond pdb=" C16 BJX E1602 " pdb=" N1 BJX E1602 " ideal model delta sigma weight residual 1.344 1.461 -0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" N BJX E1602 " pdb=" C6 BJX E1602 " ideal model delta sigma weight residual 1.412 1.515 -0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C21 BJX E1602 " pdb=" O1 BJX E1602 " ideal model delta sigma weight residual 1.347 1.422 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C5 BJX E1602 " pdb=" N1 BJX E1602 " ideal model delta sigma weight residual 1.446 1.515 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C5 BJX E1602 " pdb=" C7 BJX E1602 " ideal model delta sigma weight residual 1.518 1.585 -0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 21720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 29234 2.13 - 4.26: 289 4.26 - 6.39: 59 6.39 - 8.52: 10 8.52 - 10.65: 1 Bond angle restraints: 29593 Sorted by residual: angle pdb=" C16 BJX E1602 " pdb=" N1 BJX E1602 " pdb=" C5 BJX E1602 " ideal model delta sigma weight residual 123.13 133.78 -10.65 3.00e+00 1.11e-01 1.26e+01 angle pdb=" C LEU B 270 " pdb=" N ALA B 271 " pdb=" CA ALA B 271 " ideal model delta sigma weight residual 120.97 113.73 7.24 2.84e+00 1.24e-01 6.49e+00 angle pdb=" N ILE E 60 " pdb=" CA ILE E 60 " pdb=" C ILE E 60 " ideal model delta sigma weight residual 112.98 109.86 3.12 1.25e+00 6.40e-01 6.23e+00 angle pdb=" C8 65I E1610 " pdb=" C7 65I E1610 " pdb=" O6 65I E1610 " ideal model delta sigma weight residual 104.59 111.85 -7.26 3.00e+00 1.11e-01 5.85e+00 angle pdb=" C8 65I E1606 " pdb=" C7 65I E1606 " pdb=" O6 65I E1606 " ideal model delta sigma weight residual 104.59 111.82 -7.23 3.00e+00 1.11e-01 5.81e+00 ... (remaining 29588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 12687 35.64 - 71.29: 367 71.29 - 106.93: 71 106.93 - 142.58: 30 142.58 - 178.22: 17 Dihedral angle restraints: 13172 sinusoidal: 5071 harmonic: 8101 Sorted by residual: dihedral pdb=" CB P5S D 402 " pdb=" OG P5S D 402 " pdb=" P12 P5S D 402 " pdb=" O15 P5S D 402 " ideal model delta sinusoidal sigma weight residual -179.59 -1.37 -178.22 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB P5S D 402 " pdb=" OG P5S D 402 " pdb=" P12 P5S D 402 " pdb=" O16 P5S D 402 " ideal model delta sinusoidal sigma weight residual -64.32 113.35 -177.67 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB P5S D 402 " pdb=" OG P5S D 402 " pdb=" P12 P5S D 402 " pdb=" O13 P5S D 402 " ideal model delta sinusoidal sigma weight residual 47.21 -138.16 -174.63 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 13169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3205 0.075 - 0.150: 311 0.150 - 0.224: 0 0.224 - 0.299: 7 0.299 - 0.374: 1 Chirality restraints: 3524 Sorted by residual: chirality pdb=" C2 P5S B 403 " pdb=" C1 P5S B 403 " pdb=" C3 P5S B 403 " pdb=" O37 P5S B 403 " both_signs ideal model delta sigma weight residual False 2.59 2.22 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" C2 P5S C 403 " pdb=" C1 P5S C 403 " pdb=" C3 P5S C 403 " pdb=" O37 P5S C 403 " both_signs ideal model delta sigma weight residual False 2.59 2.30 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C2 P5S E1607 " pdb=" C1 P5S E1607 " pdb=" C3 P5S E1607 " pdb=" O37 P5S E1607 " both_signs ideal model delta sigma weight residual False 2.59 2.30 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 3521 not shown) Planarity restraints: 3637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 588 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO E 589 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO E 589 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 589 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 316 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO E 317 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO E 317 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 317 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 225 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO D 226 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 226 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 226 " -0.019 5.00e-02 4.00e+02 ... (remaining 3634 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 6155 2.82 - 3.40: 23436 3.40 - 3.98: 38575 3.98 - 4.56: 55148 4.56 - 5.14: 80787 Nonbonded interactions: 204101 Sorted by model distance: nonbonded pdb=" O SER E 541 " pdb=" OG SER E1083 " model vdw 2.235 3.040 nonbonded pdb=" O CYS B 110 " pdb=" OG1 THR B 139 " model vdw 2.242 3.040 nonbonded pdb=" OE1 GLN E 219 " pdb=" NE1 TRP E 232 " model vdw 2.260 3.120 nonbonded pdb=" OD2 ASP B 58 " pdb=" NH1 ARG C 206 " model vdw 2.271 3.120 nonbonded pdb=" O THR E 726 " pdb=" NH2 ARG E 767 " model vdw 2.276 3.120 ... (remaining 204096 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 53 or (resid 54 and (name N or name CA or name \ C or name O or name CB )) or resid 55 or (resid 56 and (name N or name CA or nam \ e C or name O or name CB )) or resid 57 through 69 or (resid 70 and (name N or n \ ame CA or name C or name O or name CB )) or resid 71 through 72 or (resid 73 and \ (name N or name CA or name C or name O or name CB )) or resid 74 through 98 or \ (resid 99 through 101 and (name N or name CA or name C or name O or name CB )) o \ r resid 102 through 105 or (resid 106 and (name N or name CA or name C or name O \ or name CB )) or resid 107 through 322 or (resid 323 and (name N or name CA or \ name C or name O or name CB )) or resid 324 or (resid 325 and (name N or name CA \ or name C or name O or name CB )) or resid 326 through 331 or (resid 332 and (n \ ame N or name CA or name C or name O or name CB )) or resid 333 through 347 or ( \ resid 348 and (name N or name CA or name C or name O or name CB )) or resid 349 \ through 360)) selection = (chain 'B' and ((resid 30 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 46 or (resid 47 and (name N or na \ me CA or name C or name O or name CB )) or resid 48 through 53 or (resid 54 and \ (name N or name CA or name C or name O or name CB )) or resid 55 or (resid 56 an \ d (name N or name CA or name C or name O or name CB )) or resid 57 through 69 or \ (resid 70 and (name N or name CA or name C or name O or name CB )) or resid 71 \ through 72 or (resid 73 and (name N or name CA or name C or name O or name CB )) \ or resid 74 through 87 or (resid 88 and (name N or name CA or name C or name O \ or name CB )) or resid 89 through 98 or (resid 99 through 101 and (name N or nam \ e CA or name C or name O or name CB )) or resid 102 through 105 or (resid 106 an \ d (name N or name CA or name C or name O or name CB )) or resid 107 through 125 \ or (resid 126 and (name N or name CA or name C or name O or name CB )) or resid \ 127 through 331 or (resid 332 and (name N or name CA or name C or name O or name \ CB )) or resid 333 through 338 or (resid 339 and (name N or name CA or name C o \ r name O or name CB )) or resid 340 through 343 or (resid 344 and (name N or nam \ e CA or name C or name O or name CB )) or resid 345 through 347 or (resid 348 an \ d (name N or name CA or name C or name O or name CB )) or resid 349 through 352 \ or (resid 353 through 360 and (name N or name CA or name C or name O or name CB \ )))) selection = (chain 'C' and ((resid 30 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 46 or (resid 47 and (name N or na \ me CA or name C or name O or name CB )) or resid 48 through 72 or (resid 73 and \ (name N or name CA or name C or name O or name CB )) or resid 74 through 87 or ( \ resid 88 and (name N or name CA or name C or name O or name CB )) or resid 89 th \ rough 125 or (resid 126 and (name N or name CA or name C or name O or name CB )) \ or resid 127 through 322 or (resid 323 and (name N or name CA or name C or name \ O or name CB )) or resid 324 or (resid 325 and (name N or name CA or name C or \ name O or name CB )) or resid 326 through 331 or (resid 332 and (name N or name \ CA or name C or name O or name CB )) or resid 333 through 338 or (resid 339 and \ (name N or name CA or name C or name O or name CB )) or resid 340 through 343 or \ (resid 344 and (name N or name CA or name C or name O or name CB )) or resid 34 \ 5 through 347 or (resid 348 and (name N or name CA or name C or name O or name C \ B )) or resid 349 through 351 or (resid 352 through 360 and (name N or name CA o \ r name C or name O or name CB )))) selection = (chain 'D' and ((resid 30 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 46 or (resid 47 and (name N or na \ me CA or name C or name O or name CB )) or resid 48 through 53 or (resid 54 and \ (name N or name CA or name C or name O or name CB )) or resid 55 or (resid 56 an \ d (name N or name CA or name C or name O or name CB )) or resid 57 through 69 or \ (resid 70 and (name N or name CA or name C or name O or name CB )) or resid 71 \ through 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) \ or resid 89 through 98 or (resid 99 through 101 and (name N or name CA or name \ C or name O or name CB )) or resid 102 through 105 or (resid 106 and (name N or \ name CA or name C or name O or name CB )) or resid 107 through 125 or (resid 126 \ and (name N or name CA or name C or name O or name CB )) or resid 127 through 3 \ 22 or (resid 323 and (name N or name CA or name C or name O or name CB )) or res \ id 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) or \ resid 326 through 338 or (resid 339 and (name N or name CA or name C or name O \ or name CB )) or resid 340 through 360)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 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: 0.010 Extract box with map and model: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 49.340 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 21732 Z= 0.175 Angle : 0.554 10.647 29609 Z= 0.256 Chirality : 0.044 0.374 3524 Planarity : 0.003 0.038 3636 Dihedral : 19.667 178.225 7891 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.39 % Allowed : 7.52 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 2770 helix: 1.06 (0.14), residues: 1318 sheet: -1.56 (0.31), residues: 291 loop : -1.13 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E1297 HIS 0.003 0.001 HIS D 234 PHE 0.013 0.001 PHE C 75 TYR 0.010 0.001 TYR D 268 ARG 0.003 0.000 ARG E 168 Details of bonding type rmsd link_NAG-ASN : bond 0.00134 ( 1) link_NAG-ASN : angle 2.18180 ( 3) link_BETA1-4 : bond 0.00337 ( 1) link_BETA1-4 : angle 2.31435 ( 3) hydrogen bonds : bond 0.24426 ( 1168) hydrogen bonds : angle 7.91317 ( 3414) SS BOND : bond 0.00266 ( 5) SS BOND : angle 0.70956 ( 10) covalent geometry : bond 0.00383 (21725) covalent geometry : angle 0.55345 (29593) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 588 time to evaluate : 2.218 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8570 (pt) REVERT: A 82 SER cc_start: 0.9228 (t) cc_final: 0.8936 (t) REVERT: A 124 SER cc_start: 0.9317 (t) cc_final: 0.9099 (t) REVERT: A 280 ASP cc_start: 0.7732 (t0) cc_final: 0.7297 (t0) REVERT: A 314 ARG cc_start: 0.8226 (ttm170) cc_final: 0.7867 (ttm170) REVERT: A 333 PHE cc_start: 0.9387 (t80) cc_final: 0.9077 (t80) REVERT: B 56 LEU cc_start: 0.6650 (OUTLIER) cc_final: 0.6224 (tm) REVERT: B 66 LEU cc_start: 0.8641 (mt) cc_final: 0.8418 (mt) REVERT: B 137 MET cc_start: 0.8976 (mtm) cc_final: 0.8577 (mtm) REVERT: B 186 HIS cc_start: 0.8407 (OUTLIER) cc_final: 0.7213 (p-80) REVERT: B 311 TRP cc_start: 0.8470 (t-100) cc_final: 0.8150 (t60) REVERT: C 163 MET cc_start: 0.8345 (mmp) cc_final: 0.8055 (mmp) REVERT: C 199 MET cc_start: 0.8958 (mtm) cc_final: 0.8754 (mtp) REVERT: C 238 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8706 (mm) REVERT: D 43 ASN cc_start: 0.8357 (t0) cc_final: 0.7436 (t0) REVERT: D 79 PHE cc_start: 0.8638 (m-80) cc_final: 0.8437 (m-10) REVERT: E 16 ARG cc_start: 0.8474 (tpp80) cc_final: 0.8208 (tpp80) REVERT: E 506 MET cc_start: 0.7229 (tpt) cc_final: 0.6885 (tpt) REVERT: E 1200 LEU cc_start: 0.9456 (tp) cc_final: 0.9185 (tp) REVERT: E 1348 GLN cc_start: 0.6813 (OUTLIER) cc_final: 0.6310 (pp30) outliers start: 47 outliers final: 24 residues processed: 620 average time/residue: 0.3248 time to fit residues: 315.4815 Evaluate side-chains 544 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 515 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 430 TRP Chi-restraints excluded: chain E residue 1309 LEU Chi-restraints excluded: chain E residue 1348 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 9.9990 chunk 210 optimal weight: 30.0000 chunk 116 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 217 optimal weight: 0.0370 chunk 84 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 162 optimal weight: 8.9990 chunk 252 optimal weight: 20.0000 overall best weight: 4.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 278 HIS B 46 HIS B 173 GLN B 175 HIS B 277 HIS B 278 HIS B 348 GLN C 128 GLN C 193 HIS C 313 GLN C 335 ASN D 41 ASN D 152 GLN D 234 HIS D 235 GLN D 313 GLN E 126 ASN E 273 GLN E 293 HIS E 326 HIS E 349 GLN E 500 ASN ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1020 GLN ** E1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1488 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.179254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.148037 restraints weight = 25613.392| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.89 r_work: 0.3458 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 21732 Z= 0.204 Angle : 0.601 9.720 29609 Z= 0.310 Chirality : 0.046 0.327 3524 Planarity : 0.005 0.049 3636 Dihedral : 21.761 166.143 3930 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.69 % Allowed : 11.24 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2770 helix: 1.45 (0.14), residues: 1357 sheet: -1.30 (0.32), residues: 266 loop : -1.39 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 51 HIS 0.010 0.001 HIS C 193 PHE 0.029 0.002 PHE B 75 TYR 0.023 0.002 TYR D 258 ARG 0.004 0.001 ARG E1487 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 1) link_NAG-ASN : angle 2.10012 ( 3) link_BETA1-4 : bond 0.00018 ( 1) link_BETA1-4 : angle 4.05008 ( 3) hydrogen bonds : bond 0.05459 ( 1168) hydrogen bonds : angle 5.21079 ( 3414) SS BOND : bond 0.00237 ( 5) SS BOND : angle 0.85555 ( 10) covalent geometry : bond 0.00461 (21725) covalent geometry : angle 0.59893 (29593) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 526 time to evaluate : 2.077 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8738 (pt) REVERT: A 280 ASP cc_start: 0.7868 (t0) cc_final: 0.7534 (t0) REVERT: A 314 ARG cc_start: 0.8653 (ttm170) cc_final: 0.8314 (ttp-170) REVERT: B 137 MET cc_start: 0.9009 (mtm) cc_final: 0.8526 (mtm) REVERT: B 186 HIS cc_start: 0.8546 (OUTLIER) cc_final: 0.7327 (p-80) REVERT: B 217 MET cc_start: 0.9115 (mtp) cc_final: 0.8869 (mtp) REVERT: B 235 GLN cc_start: 0.8687 (mt0) cc_final: 0.8435 (mt0) REVERT: B 311 TRP cc_start: 0.8545 (t-100) cc_final: 0.8160 (t60) REVERT: B 347 ARG cc_start: 0.8318 (ttm170) cc_final: 0.8109 (ttm170) REVERT: C 163 MET cc_start: 0.8129 (mmp) cc_final: 0.7830 (mmp) REVERT: C 199 MET cc_start: 0.9021 (mtm) cc_final: 0.8484 (mtp) REVERT: C 238 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8853 (mm) REVERT: C 304 TYR cc_start: 0.9318 (m-80) cc_final: 0.9103 (m-80) REVERT: D 43 ASN cc_start: 0.8627 (t0) cc_final: 0.7480 (t0) REVERT: E 253 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8286 (tp) REVERT: E 299 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8956 (mp) REVERT: E 781 ASN cc_start: 0.7582 (p0) cc_final: 0.7307 (p0) REVERT: E 785 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7347 (tm-30) REVERT: E 1021 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7577 (mm) REVERT: E 1200 LEU cc_start: 0.9392 (tp) cc_final: 0.9181 (tp) REVERT: E 1305 MET cc_start: 0.8532 (tpp) cc_final: 0.8050 (tpp) REVERT: E 1348 GLN cc_start: 0.6562 (OUTLIER) cc_final: 0.6178 (pp30) outliers start: 112 outliers final: 70 residues processed: 586 average time/residue: 0.3369 time to fit residues: 310.4044 Evaluate side-chains 581 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 504 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 519 CYS Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 557 ILE Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 1015 LEU Chi-restraints excluded: chain E residue 1021 LEU Chi-restraints excluded: chain E residue 1069 THR Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1348 GLN Chi-restraints excluded: chain E residue 1532 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 97 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 169 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 255 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 313 GLN D 128 GLN E 326 HIS ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1224 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.181153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.150033 restraints weight = 25510.120| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.90 r_work: 0.3477 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21732 Z= 0.153 Angle : 0.567 9.678 29609 Z= 0.284 Chirality : 0.045 0.313 3524 Planarity : 0.004 0.039 3636 Dihedral : 20.233 175.656 3915 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.64 % Allowed : 13.01 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.16), residues: 2770 helix: 1.61 (0.14), residues: 1363 sheet: -1.47 (0.31), residues: 285 loop : -1.35 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 75 HIS 0.011 0.001 HIS B 278 PHE 0.028 0.002 PHE B 75 TYR 0.024 0.002 TYR D 258 ARG 0.004 0.001 ARG E 598 Details of bonding type rmsd link_NAG-ASN : bond 0.00127 ( 1) link_NAG-ASN : angle 2.17382 ( 3) link_BETA1-4 : bond 0.00686 ( 1) link_BETA1-4 : angle 4.21678 ( 3) hydrogen bonds : bond 0.04639 ( 1168) hydrogen bonds : angle 4.80975 ( 3414) SS BOND : bond 0.00195 ( 5) SS BOND : angle 0.69909 ( 10) covalent geometry : bond 0.00341 (21725) covalent geometry : angle 0.56472 (29593) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 513 time to evaluate : 2.103 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8381 (pt) REVERT: A 313 GLN cc_start: 0.8855 (mt0) cc_final: 0.8521 (mt0) REVERT: A 314 ARG cc_start: 0.8787 (ttm170) cc_final: 0.8370 (ttm170) REVERT: B 137 MET cc_start: 0.9028 (mtm) cc_final: 0.8578 (mtm) REVERT: B 186 HIS cc_start: 0.8487 (OUTLIER) cc_final: 0.7370 (p-80) REVERT: B 217 MET cc_start: 0.9061 (mtp) cc_final: 0.8838 (mtp) REVERT: B 235 GLN cc_start: 0.8656 (mt0) cc_final: 0.8366 (mt0) REVERT: B 311 TRP cc_start: 0.8526 (t-100) cc_final: 0.8177 (t60) REVERT: C 163 MET cc_start: 0.8107 (mmp) cc_final: 0.7833 (mmp) REVERT: C 199 MET cc_start: 0.8990 (mtm) cc_final: 0.8549 (mtp) REVERT: C 238 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8843 (mm) REVERT: D 43 ASN cc_start: 0.8607 (t0) cc_final: 0.7445 (t0) REVERT: D 52 GLN cc_start: 0.7796 (mp10) cc_final: 0.6972 (mp10) REVERT: D 80 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9007 (mp) REVERT: D 137 MET cc_start: 0.8902 (ttp) cc_final: 0.8501 (ttp) REVERT: D 195 ARG cc_start: 0.7987 (tpp-160) cc_final: 0.7555 (tpp-160) REVERT: D 301 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8640 (mtm110) REVERT: E 264 GLN cc_start: 0.8268 (mt0) cc_final: 0.7776 (mt0) REVERT: E 299 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8873 (mp) REVERT: E 781 ASN cc_start: 0.7665 (p0) cc_final: 0.7407 (p0) REVERT: E 785 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7249 (tm-30) REVERT: E 1021 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7542 (mm) REVERT: E 1197 GLN cc_start: 0.8417 (pp30) cc_final: 0.8150 (pp30) REVERT: E 1200 LEU cc_start: 0.9399 (tp) cc_final: 0.9189 (tp) REVERT: E 1305 MET cc_start: 0.8584 (tpp) cc_final: 0.8344 (tpp) REVERT: E 1348 GLN cc_start: 0.6623 (OUTLIER) cc_final: 0.6108 (pp30) outliers start: 111 outliers final: 78 residues processed: 574 average time/residue: 0.3282 time to fit residues: 297.0007 Evaluate side-chains 584 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 498 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 301 ARG Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 519 CYS Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 557 ILE Chi-restraints excluded: chain E residue 1015 LEU Chi-restraints excluded: chain E residue 1021 LEU Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain E residue 1071 LEU Chi-restraints excluded: chain E residue 1083 SER Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1315 ILE Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1348 GLN Chi-restraints excluded: chain E residue 1424 ILE Chi-restraints excluded: chain E residue 1532 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 20 optimal weight: 8.9990 chunk 274 optimal weight: 50.0000 chunk 2 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 266 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 213 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 overall best weight: 4.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 313 GLN C 335 ASN D 128 GLN D 235 GLN E 326 HIS ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1224 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.179803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.148226 restraints weight = 25987.319| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.92 r_work: 0.3460 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21732 Z= 0.191 Angle : 0.591 9.839 29609 Z= 0.296 Chirality : 0.046 0.311 3524 Planarity : 0.004 0.041 3636 Dihedral : 19.104 170.157 3911 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 6.35 % Allowed : 14.34 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.16), residues: 2770 helix: 1.54 (0.14), residues: 1369 sheet: -1.44 (0.31), residues: 285 loop : -1.36 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 91 HIS 0.010 0.001 HIS C 193 PHE 0.026 0.002 PHE B 75 TYR 0.027 0.002 TYR D 258 ARG 0.007 0.001 ARG E1145 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 1) link_NAG-ASN : angle 2.30669 ( 3) link_BETA1-4 : bond 0.00858 ( 1) link_BETA1-4 : angle 4.37846 ( 3) hydrogen bonds : bond 0.04394 ( 1168) hydrogen bonds : angle 4.66527 ( 3414) SS BOND : bond 0.00276 ( 5) SS BOND : angle 0.77389 ( 10) covalent geometry : bond 0.00437 (21725) covalent geometry : angle 0.58855 (29593) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 512 time to evaluate : 3.496 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8553 (pt) REVERT: A 52 GLN cc_start: 0.8169 (mp10) cc_final: 0.7874 (mt0) REVERT: A 205 LEU cc_start: 0.8809 (mt) cc_final: 0.8567 (mt) REVERT: A 313 GLN cc_start: 0.8915 (mt0) cc_final: 0.8445 (mt0) REVERT: B 137 MET cc_start: 0.9096 (mtm) cc_final: 0.8651 (mtm) REVERT: B 186 HIS cc_start: 0.8616 (OUTLIER) cc_final: 0.7491 (p-80) REVERT: B 235 GLN cc_start: 0.8643 (mt0) cc_final: 0.8395 (mt0) REVERT: B 311 TRP cc_start: 0.8566 (t-100) cc_final: 0.8185 (t60) REVERT: B 313 GLN cc_start: 0.7575 (mt0) cc_final: 0.7341 (mt0) REVERT: C 37 SER cc_start: 0.8460 (t) cc_final: 0.8214 (p) REVERT: C 163 MET cc_start: 0.8122 (mmp) cc_final: 0.7877 (mmp) REVERT: C 199 MET cc_start: 0.8994 (mtm) cc_final: 0.8793 (mtp) REVERT: C 238 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8835 (mm) REVERT: D 32 ARG cc_start: 0.7816 (mmm160) cc_final: 0.7493 (tpt170) REVERT: D 43 ASN cc_start: 0.8607 (t0) cc_final: 0.7466 (t0) REVERT: D 52 GLN cc_start: 0.7815 (mp10) cc_final: 0.7039 (mp10) REVERT: D 80 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9109 (mp) REVERT: D 195 ARG cc_start: 0.7993 (tpp-160) cc_final: 0.7593 (tpp-160) REVERT: D 301 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8594 (mtm110) REVERT: D 325 ARG cc_start: 0.8145 (ptp-170) cc_final: 0.7883 (ptp-170) REVERT: E 216 ARG cc_start: 0.8038 (ttm-80) cc_final: 0.7713 (ttp-110) REVERT: E 299 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8858 (mp) REVERT: E 781 ASN cc_start: 0.7724 (p0) cc_final: 0.7355 (p0) REVERT: E 785 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7214 (tm-30) REVERT: E 1021 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7591 (mm) REVERT: E 1105 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7610 (mm) REVERT: E 1197 GLN cc_start: 0.8507 (pp30) cc_final: 0.8248 (pp30) REVERT: E 1200 LEU cc_start: 0.9431 (tp) cc_final: 0.9222 (tp) REVERT: E 1348 GLN cc_start: 0.6586 (OUTLIER) cc_final: 0.6228 (pp30) outliers start: 125 outliers final: 96 residues processed: 579 average time/residue: 0.3888 time to fit residues: 355.1603 Evaluate side-chains 598 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 493 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 301 ARG Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 519 CYS Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 557 ILE Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 788 ILE Chi-restraints excluded: chain E residue 1015 LEU Chi-restraints excluded: chain E residue 1021 LEU Chi-restraints excluded: chain E residue 1067 VAL Chi-restraints excluded: chain E residue 1071 LEU Chi-restraints excluded: chain E residue 1083 SER Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1315 ILE Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1348 GLN Chi-restraints excluded: chain E residue 1424 ILE Chi-restraints excluded: chain E residue 1532 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 76 optimal weight: 0.0570 chunk 26 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 267 optimal weight: 40.0000 chunk 130 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 156 optimal weight: 10.0000 chunk 243 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 overall best weight: 4.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 HIS C 313 GLN D 128 GLN E 326 HIS ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1224 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.178378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.147726 restraints weight = 25848.777| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.87 r_work: 0.3464 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21732 Z= 0.188 Angle : 0.589 10.003 29609 Z= 0.294 Chirality : 0.046 0.305 3524 Planarity : 0.004 0.041 3636 Dihedral : 18.409 166.381 3911 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 6.66 % Allowed : 15.20 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 2770 helix: 1.53 (0.14), residues: 1371 sheet: -1.47 (0.30), residues: 290 loop : -1.38 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 91 HIS 0.009 0.001 HIS C 193 PHE 0.023 0.002 PHE C 75 TYR 0.027 0.002 TYR D 258 ARG 0.005 0.001 ARG E1145 Details of bonding type rmsd link_NAG-ASN : bond 0.00118 ( 1) link_NAG-ASN : angle 2.53820 ( 3) link_BETA1-4 : bond 0.00900 ( 1) link_BETA1-4 : angle 4.35760 ( 3) hydrogen bonds : bond 0.04280 ( 1168) hydrogen bonds : angle 4.59927 ( 3414) SS BOND : bond 0.00288 ( 5) SS BOND : angle 0.59615 ( 10) covalent geometry : bond 0.00430 (21725) covalent geometry : angle 0.58722 (29593) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 497 time to evaluate : 2.017 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8474 (pt) REVERT: A 52 GLN cc_start: 0.8129 (mp10) cc_final: 0.7880 (mt0) REVERT: A 205 LEU cc_start: 0.8793 (mt) cc_final: 0.8544 (mt) REVERT: A 313 GLN cc_start: 0.8954 (mt0) cc_final: 0.8594 (mt0) REVERT: B 137 MET cc_start: 0.9077 (mtm) cc_final: 0.8628 (mtm) REVERT: B 186 HIS cc_start: 0.8369 (OUTLIER) cc_final: 0.6963 (p90) REVERT: B 217 MET cc_start: 0.9171 (mtp) cc_final: 0.8957 (mtp) REVERT: B 235 GLN cc_start: 0.8616 (mt0) cc_final: 0.8404 (mt0) REVERT: B 311 TRP cc_start: 0.8562 (t-100) cc_final: 0.8185 (t60) REVERT: B 313 GLN cc_start: 0.7565 (mt0) cc_final: 0.7343 (mt0) REVERT: C 37 SER cc_start: 0.8476 (t) cc_final: 0.8245 (p) REVERT: C 63 LEU cc_start: 0.9212 (mt) cc_final: 0.9010 (mt) REVERT: C 163 MET cc_start: 0.8169 (mmp) cc_final: 0.7957 (mmp) REVERT: C 199 MET cc_start: 0.8978 (mtm) cc_final: 0.8717 (mtp) REVERT: D 32 ARG cc_start: 0.7782 (mmm160) cc_final: 0.7540 (tpt170) REVERT: D 43 ASN cc_start: 0.8659 (t0) cc_final: 0.7651 (t0) REVERT: D 80 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9107 (mp) REVERT: D 206 ARG cc_start: 0.8528 (mmt90) cc_final: 0.8057 (mmt90) REVERT: D 301 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8560 (mtm110) REVERT: D 325 ARG cc_start: 0.8134 (ptp-170) cc_final: 0.7851 (ptp-170) REVERT: E 216 ARG cc_start: 0.8034 (ttm-80) cc_final: 0.7703 (ttp-110) REVERT: E 253 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8295 (tp) REVERT: E 299 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8834 (mp) REVERT: E 400 MET cc_start: 0.8428 (mmt) cc_final: 0.8049 (mmt) REVERT: E 781 ASN cc_start: 0.7779 (p0) cc_final: 0.7449 (p0) REVERT: E 785 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7271 (tm-30) REVERT: E 1021 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7565 (mm) REVERT: E 1197 GLN cc_start: 0.8597 (pp30) cc_final: 0.8291 (pp30) REVERT: E 1200 LEU cc_start: 0.9433 (tp) cc_final: 0.9224 (tp) REVERT: E 1348 GLN cc_start: 0.6640 (OUTLIER) cc_final: 0.6295 (pp30) outliers start: 131 outliers final: 99 residues processed: 569 average time/residue: 0.3205 time to fit residues: 286.3591 Evaluate side-chains 588 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 481 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 301 ARG Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 519 CYS Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 557 ILE Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 788 ILE Chi-restraints excluded: chain E residue 1015 LEU Chi-restraints excluded: chain E residue 1021 LEU Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain E residue 1069 THR Chi-restraints excluded: chain E residue 1071 LEU Chi-restraints excluded: chain E residue 1083 SER Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1315 ILE Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1348 GLN Chi-restraints excluded: chain E residue 1424 ILE Chi-restraints excluded: chain E residue 1532 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 131 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 237 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 161 optimal weight: 9.9990 chunk 154 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 262 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 73 optimal weight: 8.9990 chunk 272 optimal weight: 40.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS B 247 ASN B 278 HIS C 128 GLN D 128 GLN E 264 GLN E 282 GLN E 326 HIS ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.175036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.143770 restraints weight = 25851.352| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.89 r_work: 0.3409 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 21732 Z= 0.310 Angle : 0.701 10.243 29609 Z= 0.353 Chirality : 0.050 0.318 3524 Planarity : 0.005 0.054 3636 Dihedral : 18.168 171.616 3909 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 7.37 % Allowed : 16.42 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.16), residues: 2770 helix: 1.12 (0.14), residues: 1373 sheet: -1.65 (0.30), residues: 283 loop : -1.57 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 91 HIS 0.009 0.001 HIS C 193 PHE 0.033 0.002 PHE C 75 TYR 0.030 0.002 TYR D 258 ARG 0.005 0.001 ARG E1145 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 1) link_NAG-ASN : angle 2.69174 ( 3) link_BETA1-4 : bond 0.00950 ( 1) link_BETA1-4 : angle 4.46034 ( 3) hydrogen bonds : bond 0.04791 ( 1168) hydrogen bonds : angle 4.85796 ( 3414) SS BOND : bond 0.00543 ( 5) SS BOND : angle 1.67092 ( 10) covalent geometry : bond 0.00720 (21725) covalent geometry : angle 0.69837 (29593) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 514 time to evaluate : 2.208 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8677 (pt) REVERT: A 52 GLN cc_start: 0.8171 (mp10) cc_final: 0.7918 (mt0) REVERT: A 205 LEU cc_start: 0.8821 (mt) cc_final: 0.8612 (mt) REVERT: A 313 GLN cc_start: 0.9039 (mt0) cc_final: 0.8605 (mt0) REVERT: A 325 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7588 (ptp-110) REVERT: A 335 ASN cc_start: 0.8961 (m110) cc_final: 0.8714 (m110) REVERT: B 137 MET cc_start: 0.9143 (mtm) cc_final: 0.8675 (mtm) REVERT: B 186 HIS cc_start: 0.8705 (OUTLIER) cc_final: 0.7590 (p90) REVERT: B 311 TRP cc_start: 0.8615 (t-100) cc_final: 0.8174 (t60) REVERT: C 37 SER cc_start: 0.8556 (t) cc_final: 0.8326 (p) REVERT: C 163 MET cc_start: 0.8140 (mmp) cc_final: 0.7920 (mmp) REVERT: C 199 MET cc_start: 0.9038 (mtm) cc_final: 0.8626 (mtp) REVERT: D 43 ASN cc_start: 0.8659 (t0) cc_final: 0.7596 (t0) REVERT: D 80 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9173 (mp) REVERT: D 301 ARG cc_start: 0.9325 (OUTLIER) cc_final: 0.8566 (mtm110) REVERT: E 216 ARG cc_start: 0.8094 (ttm-80) cc_final: 0.7715 (ttp-110) REVERT: E 253 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8331 (tp) REVERT: E 264 GLN cc_start: 0.8292 (mt0) cc_final: 0.7925 (mt0) REVERT: E 299 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8902 (mp) REVERT: E 1021 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7571 (mm) REVERT: E 1197 GLN cc_start: 0.8703 (pp30) cc_final: 0.8366 (pp30) REVERT: E 1267 SER cc_start: 0.9231 (t) cc_final: 0.8907 (m) REVERT: E 1348 GLN cc_start: 0.6525 (OUTLIER) cc_final: 0.6139 (pp30) outliers start: 145 outliers final: 116 residues processed: 594 average time/residue: 0.3301 time to fit residues: 307.1995 Evaluate side-chains 631 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 506 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 301 ARG Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 519 CYS Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 557 ILE Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 788 ILE Chi-restraints excluded: chain E residue 848 THR Chi-restraints excluded: chain E residue 1015 LEU Chi-restraints excluded: chain E residue 1021 LEU Chi-restraints excluded: chain E residue 1022 LEU Chi-restraints excluded: chain E residue 1026 VAL Chi-restraints excluded: chain E residue 1067 VAL Chi-restraints excluded: chain E residue 1069 THR Chi-restraints excluded: chain E residue 1071 LEU Chi-restraints excluded: chain E residue 1083 SER Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1315 ILE Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1348 GLN Chi-restraints excluded: chain E residue 1424 ILE Chi-restraints excluded: chain E residue 1532 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 265 optimal weight: 50.0000 chunk 246 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 chunk 1 optimal weight: 40.0000 chunk 172 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN B 278 HIS D 128 GLN E 326 HIS ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1224 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.181046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.149573 restraints weight = 25685.709| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.93 r_work: 0.3474 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21732 Z= 0.132 Angle : 0.577 10.181 29609 Z= 0.286 Chirality : 0.045 0.292 3524 Planarity : 0.004 0.040 3636 Dihedral : 17.140 176.448 3909 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.29 % Allowed : 19.12 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.16), residues: 2770 helix: 1.56 (0.14), residues: 1371 sheet: -1.71 (0.29), residues: 295 loop : -1.40 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E1247 HIS 0.040 0.001 HIS B 278 PHE 0.033 0.002 PHE A 168 TYR 0.024 0.001 TYR D 258 ARG 0.007 0.001 ARG A 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00025 ( 1) link_NAG-ASN : angle 2.77844 ( 3) link_BETA1-4 : bond 0.01188 ( 1) link_BETA1-4 : angle 4.53404 ( 3) hydrogen bonds : bond 0.03978 ( 1168) hydrogen bonds : angle 4.51995 ( 3414) SS BOND : bond 0.00220 ( 5) SS BOND : angle 0.88322 ( 10) covalent geometry : bond 0.00294 (21725) covalent geometry : angle 0.57479 (29593) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 516 time to evaluate : 2.444 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8444 (pt) REVERT: A 313 GLN cc_start: 0.8967 (mt0) cc_final: 0.8526 (mt0) REVERT: A 314 ARG cc_start: 0.8757 (ttm170) cc_final: 0.8415 (ttm170) REVERT: B 137 MET cc_start: 0.9075 (mtm) cc_final: 0.8633 (mtm) REVERT: B 186 HIS cc_start: 0.8551 (OUTLIER) cc_final: 0.7355 (p90) REVERT: B 235 GLN cc_start: 0.8660 (mt0) cc_final: 0.8430 (mt0) REVERT: B 311 TRP cc_start: 0.8563 (t-100) cc_final: 0.8190 (t60) REVERT: B 338 LYS cc_start: 0.8683 (tppt) cc_final: 0.8410 (mmmm) REVERT: C 37 SER cc_start: 0.8531 (t) cc_final: 0.8275 (p) REVERT: D 32 ARG cc_start: 0.7759 (mmm160) cc_final: 0.7481 (tpt170) REVERT: D 43 ASN cc_start: 0.8528 (t0) cc_final: 0.7601 (t0) REVERT: D 67 LYS cc_start: 0.8437 (mptt) cc_final: 0.7876 (mptt) REVERT: D 80 LEU cc_start: 0.9430 (tp) cc_final: 0.9127 (mp) REVERT: D 206 ARG cc_start: 0.8541 (mmt90) cc_final: 0.8057 (mmt90) REVERT: D 301 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8601 (mtm110) REVERT: D 325 ARG cc_start: 0.8098 (ptp-170) cc_final: 0.7805 (ptp-170) REVERT: E 299 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8815 (mp) REVERT: E 337 LYS cc_start: 0.7651 (mtpp) cc_final: 0.7418 (mtmt) REVERT: E 400 MET cc_start: 0.8434 (mmt) cc_final: 0.8161 (mmt) REVERT: E 491 HIS cc_start: 0.7594 (OUTLIER) cc_final: 0.7043 (t70) REVERT: E 785 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7309 (tm-30) REVERT: E 1021 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7591 (mm) REVERT: E 1197 GLN cc_start: 0.8557 (pp30) cc_final: 0.8226 (pp30) REVERT: E 1348 GLN cc_start: 0.6592 (OUTLIER) cc_final: 0.6312 (pp30) outliers start: 104 outliers final: 81 residues processed: 577 average time/residue: 0.3199 time to fit residues: 287.5366 Evaluate side-chains 584 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 496 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 301 ARG Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 519 CYS Chi-restraints excluded: chain E residue 557 ILE Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 788 ILE Chi-restraints excluded: chain E residue 901 ILE Chi-restraints excluded: chain E residue 1015 LEU Chi-restraints excluded: chain E residue 1021 LEU Chi-restraints excluded: chain E residue 1022 LEU Chi-restraints excluded: chain E residue 1030 ILE Chi-restraints excluded: chain E residue 1071 LEU Chi-restraints excluded: chain E residue 1083 SER Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1315 ILE Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1348 GLN Chi-restraints excluded: chain E residue 1424 ILE Chi-restraints excluded: chain E residue 1532 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 257 optimal weight: 30.0000 chunk 54 optimal weight: 9.9990 chunk 199 optimal weight: 0.0870 chunk 226 optimal weight: 30.0000 chunk 179 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 HIS E 264 GLN E 282 GLN E 326 HIS ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1224 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.177100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.148924 restraints weight = 25805.182| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.92 r_work: 0.3451 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21732 Z= 0.184 Angle : 0.601 10.161 29609 Z= 0.299 Chirality : 0.046 0.309 3524 Planarity : 0.004 0.041 3636 Dihedral : 16.745 179.297 3909 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.90 % Allowed : 18.40 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.16), residues: 2770 helix: 1.54 (0.14), residues: 1372 sheet: -1.57 (0.30), residues: 290 loop : -1.43 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E1297 HIS 0.014 0.001 HIS C 259 PHE 0.030 0.002 PHE A 168 TYR 0.026 0.002 TYR D 258 ARG 0.006 0.001 ARG E 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00058 ( 1) link_NAG-ASN : angle 2.91805 ( 3) link_BETA1-4 : bond 0.01027 ( 1) link_BETA1-4 : angle 4.44329 ( 3) hydrogen bonds : bond 0.04114 ( 1168) hydrogen bonds : angle 4.53216 ( 3414) SS BOND : bond 0.00267 ( 5) SS BOND : angle 0.96375 ( 10) covalent geometry : bond 0.00426 (21725) covalent geometry : angle 0.59818 (29593) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 502 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8480 (pt) REVERT: A 313 GLN cc_start: 0.8954 (mt0) cc_final: 0.8466 (mt0) REVERT: A 325 ARG cc_start: 0.7692 (ptm160) cc_final: 0.7448 (ptp-110) REVERT: B 137 MET cc_start: 0.9009 (mtm) cc_final: 0.8558 (mtm) REVERT: B 186 HIS cc_start: 0.8598 (OUTLIER) cc_final: 0.7301 (p90) REVERT: B 311 TRP cc_start: 0.8559 (t-100) cc_final: 0.8145 (t60) REVERT: B 313 GLN cc_start: 0.7508 (mt0) cc_final: 0.7118 (mt0) REVERT: B 338 LYS cc_start: 0.8605 (tppt) cc_final: 0.8363 (mmmm) REVERT: C 37 SER cc_start: 0.8519 (t) cc_final: 0.8271 (p) REVERT: D 43 ASN cc_start: 0.8581 (t0) cc_final: 0.7604 (t0) REVERT: D 67 LYS cc_start: 0.8509 (mptt) cc_final: 0.7941 (mptt) REVERT: D 80 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9135 (mp) REVERT: D 137 MET cc_start: 0.8879 (ttp) cc_final: 0.8527 (ttp) REVERT: D 206 ARG cc_start: 0.8553 (mmt90) cc_final: 0.8093 (mmt90) REVERT: D 301 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8534 (mtm110) REVERT: E 264 GLN cc_start: 0.8294 (mt0) cc_final: 0.7914 (mt0) REVERT: E 299 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8785 (mp) REVERT: E 400 MET cc_start: 0.8359 (mmt) cc_final: 0.8057 (mmt) REVERT: E 491 HIS cc_start: 0.7489 (OUTLIER) cc_final: 0.6960 (t70) REVERT: E 785 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7375 (tm-30) REVERT: E 1021 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7656 (mm) REVERT: E 1197 GLN cc_start: 0.8645 (pp30) cc_final: 0.8290 (pp30) REVERT: E 1348 GLN cc_start: 0.6541 (OUTLIER) cc_final: 0.6220 (pp30) outliers start: 116 outliers final: 93 residues processed: 568 average time/residue: 0.3297 time to fit residues: 290.8041 Evaluate side-chains 599 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 498 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 259 HIS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 301 ARG Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 519 CYS Chi-restraints excluded: chain E residue 557 ILE Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 709 THR Chi-restraints excluded: chain E residue 788 ILE Chi-restraints excluded: chain E residue 901 ILE Chi-restraints excluded: chain E residue 1015 LEU Chi-restraints excluded: chain E residue 1021 LEU Chi-restraints excluded: chain E residue 1022 LEU Chi-restraints excluded: chain E residue 1030 ILE Chi-restraints excluded: chain E residue 1067 VAL Chi-restraints excluded: chain E residue 1069 THR Chi-restraints excluded: chain E residue 1071 LEU Chi-restraints excluded: chain E residue 1083 SER Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1315 ILE Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1348 GLN Chi-restraints excluded: chain E residue 1424 ILE Chi-restraints excluded: chain E residue 1532 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 195 optimal weight: 10.0000 chunk 99 optimal weight: 0.2980 chunk 94 optimal weight: 5.9990 chunk 273 optimal weight: 9.9990 chunk 203 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 237 optimal weight: 8.9990 chunk 173 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 HIS E 326 HIS ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.176059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.147931 restraints weight = 25654.011| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.86 r_work: 0.3450 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21732 Z= 0.220 Angle : 0.627 10.202 29609 Z= 0.313 Chirality : 0.047 0.310 3524 Planarity : 0.004 0.041 3636 Dihedral : 16.637 176.972 3909 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.85 % Allowed : 18.20 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2770 helix: 1.46 (0.14), residues: 1372 sheet: -1.64 (0.30), residues: 287 loop : -1.47 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 91 HIS 0.023 0.001 HIS C 259 PHE 0.027 0.002 PHE A 168 TYR 0.027 0.002 TYR D 258 ARG 0.007 0.001 ARG A 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00094 ( 1) link_NAG-ASN : angle 2.99000 ( 3) link_BETA1-4 : bond 0.01029 ( 1) link_BETA1-4 : angle 4.43120 ( 3) hydrogen bonds : bond 0.04222 ( 1168) hydrogen bonds : angle 4.58100 ( 3414) SS BOND : bond 0.00324 ( 5) SS BOND : angle 0.99240 ( 10) covalent geometry : bond 0.00510 (21725) covalent geometry : angle 0.62427 (29593) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 512 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8611 (pt) REVERT: A 313 GLN cc_start: 0.8921 (mt0) cc_final: 0.8410 (mt0) REVERT: A 325 ARG cc_start: 0.7738 (ptm160) cc_final: 0.7517 (ptp-110) REVERT: B 137 MET cc_start: 0.9012 (mtm) cc_final: 0.8552 (mtm) REVERT: B 186 HIS cc_start: 0.8650 (OUTLIER) cc_final: 0.7389 (p90) REVERT: B 311 TRP cc_start: 0.8562 (t-100) cc_final: 0.8129 (t60) REVERT: B 313 GLN cc_start: 0.7568 (mt0) cc_final: 0.7171 (mt0) REVERT: B 338 LYS cc_start: 0.8660 (tppt) cc_final: 0.8330 (mmmm) REVERT: C 37 SER cc_start: 0.8468 (t) cc_final: 0.8218 (p) REVERT: C 259 HIS cc_start: 0.7650 (OUTLIER) cc_final: 0.7118 (t70) REVERT: D 43 ASN cc_start: 0.8533 (t0) cc_final: 0.7614 (t0) REVERT: D 80 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9148 (mp) REVERT: D 137 MET cc_start: 0.8912 (ttp) cc_final: 0.8545 (ttp) REVERT: D 191 LEU cc_start: 0.8237 (tt) cc_final: 0.7989 (tp) REVERT: D 206 ARG cc_start: 0.8642 (mmt90) cc_final: 0.8222 (mmt90) REVERT: D 301 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8534 (mtm110) REVERT: D 325 ARG cc_start: 0.8175 (ptp-170) cc_final: 0.7918 (ptp-170) REVERT: E 264 GLN cc_start: 0.8260 (mt0) cc_final: 0.7991 (mt0) REVERT: E 299 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8808 (mp) REVERT: E 400 MET cc_start: 0.8368 (mmt) cc_final: 0.8106 (mmt) REVERT: E 412 MET cc_start: 0.6521 (ptp) cc_final: 0.6160 (ptp) REVERT: E 491 HIS cc_start: 0.7538 (OUTLIER) cc_final: 0.6999 (t70) REVERT: E 785 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7376 (tm-30) REVERT: E 1021 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7599 (mm) REVERT: E 1197 GLN cc_start: 0.8677 (pp30) cc_final: 0.8321 (pp30) REVERT: E 1348 GLN cc_start: 0.6522 (OUTLIER) cc_final: 0.6127 (pp30) outliers start: 115 outliers final: 99 residues processed: 576 average time/residue: 0.3306 time to fit residues: 296.6555 Evaluate side-chains 611 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 503 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 259 HIS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 301 ARG Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 519 CYS Chi-restraints excluded: chain E residue 557 ILE Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 709 THR Chi-restraints excluded: chain E residue 788 ILE Chi-restraints excluded: chain E residue 848 THR Chi-restraints excluded: chain E residue 901 ILE Chi-restraints excluded: chain E residue 1015 LEU Chi-restraints excluded: chain E residue 1021 LEU Chi-restraints excluded: chain E residue 1022 LEU Chi-restraints excluded: chain E residue 1030 ILE Chi-restraints excluded: chain E residue 1067 VAL Chi-restraints excluded: chain E residue 1069 THR Chi-restraints excluded: chain E residue 1071 LEU Chi-restraints excluded: chain E residue 1083 SER Chi-restraints excluded: chain E residue 1152 SER Chi-restraints excluded: chain E residue 1201 VAL Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1315 ILE Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1348 GLN Chi-restraints excluded: chain E residue 1424 ILE Chi-restraints excluded: chain E residue 1532 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 136 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 178 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 220 optimal weight: 0.5980 chunk 163 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 270 optimal weight: 40.0000 chunk 181 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 HIS ** E 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 GLN E 326 HIS ** E1123 ASN ** 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 = 0.3935 r_free = 0.3935 target = 0.181177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.153728 restraints weight = 25684.880| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.81 r_work: 0.3543 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 21732 Z= 0.110 Angle : 0.572 10.016 29609 Z= 0.283 Chirality : 0.045 0.455 3524 Planarity : 0.004 0.048 3636 Dihedral : 15.922 172.445 3909 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.27 % Allowed : 20.18 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.17), residues: 2770 helix: 1.90 (0.14), residues: 1359 sheet: -1.56 (0.29), residues: 300 loop : -1.26 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E1247 HIS 0.056 0.001 HIS C 259 PHE 0.027 0.001 PHE A 168 TYR 0.025 0.001 TYR D 258 ARG 0.013 0.001 ARG C 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00020 ( 1) link_NAG-ASN : angle 3.05401 ( 3) link_BETA1-4 : bond 0.00491 ( 1) link_BETA1-4 : angle 4.56642 ( 3) hydrogen bonds : bond 0.03684 ( 1168) hydrogen bonds : angle 4.33388 ( 3414) SS BOND : bond 0.00167 ( 5) SS BOND : angle 0.58244 ( 10) covalent geometry : bond 0.00229 (21725) covalent geometry : angle 0.56922 (29593) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5540 Ramachandran restraints generated. 2770 Oldfield, 0 Emsley, 2770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 521 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8333 (pt) REVERT: A 313 GLN cc_start: 0.8882 (mt0) cc_final: 0.8405 (mt0) REVERT: B 67 LYS cc_start: 0.8033 (mppt) cc_final: 0.7719 (mppt) REVERT: B 137 MET cc_start: 0.8862 (mtm) cc_final: 0.8611 (mtm) REVERT: B 186 HIS cc_start: 0.8339 (OUTLIER) cc_final: 0.7146 (p90) REVERT: B 311 TRP cc_start: 0.8553 (t-100) cc_final: 0.8154 (t60) REVERT: B 313 GLN cc_start: 0.7322 (mt0) cc_final: 0.6818 (mt0) REVERT: B 335 ASN cc_start: 0.7840 (m-40) cc_final: 0.7590 (m-40) REVERT: B 336 THR cc_start: 0.8472 (p) cc_final: 0.8257 (p) REVERT: B 338 LYS cc_start: 0.8655 (tppt) cc_final: 0.8377 (mmmm) REVERT: C 37 SER cc_start: 0.8401 (t) cc_final: 0.8156 (p) REVERT: C 180 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8779 (p) REVERT: D 43 ASN cc_start: 0.8428 (t0) cc_final: 0.7589 (t0) REVERT: D 80 LEU cc_start: 0.9435 (tp) cc_final: 0.9155 (mp) REVERT: D 137 MET cc_start: 0.8857 (ttp) cc_final: 0.8416 (ttp) REVERT: D 191 LEU cc_start: 0.8275 (tt) cc_final: 0.7987 (tp) REVERT: D 206 ARG cc_start: 0.8568 (mmt90) cc_final: 0.8180 (mmt90) REVERT: D 325 ARG cc_start: 0.8120 (ptp-170) cc_final: 0.7860 (ptp-170) REVERT: E 123 TYR cc_start: 0.8943 (t80) cc_final: 0.8689 (t80) REVERT: E 299 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8667 (mp) REVERT: E 412 MET cc_start: 0.6397 (ptp) cc_final: 0.6042 (ptp) REVERT: E 491 HIS cc_start: 0.7347 (OUTLIER) cc_final: 0.6921 (t70) REVERT: E 506 MET cc_start: 0.6890 (tpt) cc_final: 0.6528 (tpp) REVERT: E 507 LYS cc_start: 0.6869 (mmtm) cc_final: 0.6430 (mmmt) REVERT: E 547 ASN cc_start: 0.8871 (t0) cc_final: 0.8274 (t0) REVERT: E 785 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7272 (tm-30) REVERT: E 1105 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7142 (mm) REVERT: E 1197 GLN cc_start: 0.8570 (pp30) cc_final: 0.8197 (pp30) REVERT: E 1215 ARG cc_start: 0.8198 (mtm-85) cc_final: 0.7692 (mtt180) REVERT: E 1348 GLN cc_start: 0.6571 (OUTLIER) cc_final: 0.6229 (pp30) outliers start: 84 outliers final: 68 residues processed: 571 average time/residue: 0.3321 time to fit residues: 294.3361 Evaluate side-chains 579 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 504 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 491 HIS Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 788 ILE Chi-restraints excluded: chain E residue 1015 LEU Chi-restraints excluded: chain E residue 1030 ILE Chi-restraints excluded: chain E residue 1067 VAL Chi-restraints excluded: chain E residue 1083 SER Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1315 ILE Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1348 GLN Chi-restraints excluded: chain E residue 1424 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 131 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 205 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 228 optimal weight: 5.9990 chunk 164 optimal weight: 20.0000 chunk 68 optimal weight: 30.0000 chunk 73 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 128 GLN E 264 GLN E 326 HIS ** E 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1123 ASN ** 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 = 0.3866 r_free = 0.3866 target = 0.174525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.145997 restraints weight = 25945.559| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.89 r_work: 0.3416 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 21732 Z= 0.301 Angle : 0.695 10.166 29609 Z= 0.349 Chirality : 0.050 0.327 3524 Planarity : 0.005 0.051 3636 Dihedral : 16.211 169.577 3908 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.88 % Allowed : 20.34 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2770 helix: 1.40 (0.14), residues: 1371 sheet: -1.62 (0.30), residues: 287 loop : -1.49 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 311 HIS 0.011 0.001 HIS C 259 PHE 0.032 0.002 PHE C 75 TYR 0.035 0.003 TYR B 304 ARG 0.012 0.001 ARG C 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00127 ( 1) link_NAG-ASN : angle 3.29890 ( 3) link_BETA1-4 : bond 0.00957 ( 1) link_BETA1-4 : angle 4.27095 ( 3) hydrogen bonds : bond 0.04497 ( 1168) hydrogen bonds : angle 4.65425 ( 3414) SS BOND : bond 0.00406 ( 5) SS BOND : angle 1.13582 ( 10) covalent geometry : bond 0.00695 (21725) covalent geometry : angle 0.69267 (29593) =============================================================================== Job complete usr+sys time: 12692.92 seconds wall clock time: 219 minutes 15.12 seconds (13155.12 seconds total)