Starting phenix.real_space_refine on Thu Apr 11 03:00:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tys_26193/04_2024/7tys_26193_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tys_26193/04_2024/7tys_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tys_26193/04_2024/7tys_26193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tys_26193/04_2024/7tys_26193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tys_26193/04_2024/7tys_26193_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tys_26193/04_2024/7tys_26193_updated.pdb" } 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 Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 10.57, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 9.25 Conformation dependent library (CDL) restraints added in 4.1 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... running ksdssp... Secondary structure from input PDB file: 93 helices and 25 sheets defined 47.8% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.91 Creating SS restraints... Processing helix chain 'A' and resid 26 through 29 removed outlier: 3.523A pdb=" N ARG A 29 " --> pdb=" O TYR A 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 26 through 29' Processing helix chain 'A' and resid 54 through 57 No H-bonds generated for 'chain 'A' and resid 54 through 57' Processing helix chain 'A' and resid 59 through 65 removed outlier: 3.663A pdb=" N VAL A 64 " --> pdb=" O PHE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 97 removed outlier: 3.569A pdb=" N SER A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 171 removed outlier: 3.693A pdb=" N LEU A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'B' and resid 54 through 57 No H-bonds generated for 'chain 'B' and resid 54 through 57' Processing helix chain 'B' and resid 59 through 65 Processing helix chain 'B' and resid 68 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 117 through 129 Processing helix chain 'B' and resid 143 through 171 Processing helix chain 'B' and resid 175 through 180 removed outlier: 3.776A pdb=" N GLU B 179 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR B 180 " --> pdb=" O ARG B 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 175 through 180' Processing helix chain 'B' and resid 266 through 269 removed outlier: 4.276A pdb=" N ASP B 269 " --> pdb=" O PRO B 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 269' Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 346 through 361 Processing helix chain 'C' and resid 54 through 57 No H-bonds generated for 'chain 'C' and resid 54 through 57' Processing helix chain 'C' and resid 59 through 65 Processing helix chain 'C' and resid 68 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 117 through 128 Processing helix chain 'C' and resid 143 through 171 Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing helix chain 'C' and resid 346 through 360 Processing helix chain 'D' and resid 54 through 57 No H-bonds generated for 'chain 'D' and resid 54 through 57' Processing helix chain 'D' and resid 59 through 65 Processing helix chain 'D' and resid 68 through 97 Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 143 through 171 Processing helix chain 'D' and resid 175 through 180 removed outlier: 3.560A pdb=" N GLU D 179 " --> pdb=" O HIS D 175 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR D 180 " --> pdb=" O ARG D 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 175 through 180' Processing helix chain 'D' and resid 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 346 through 359 Processing helix chain 'E' and resid 9 through 12 No H-bonds generated for 'chain 'E' and resid 9 through 12' Processing helix chain 'E' and resid 21 through 23 No H-bonds generated for 'chain 'E' and resid 21 through 23' Processing helix chain 'E' and resid 27 through 56 removed outlier: 3.572A pdb=" N VAL E 33 " --> pdb=" O ASP E 29 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Proline residue: E 35 - end of helix 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 removed outlier: 4.132A pdb=" N SER E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 71 through 97 removed outlier: 4.014A pdb=" N GLY E 97 " --> pdb=" O ILE E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 106 No H-bonds generated for 'chain 'E' and resid 104 through 106' Processing helix chain 'E' and resid 108 through 129 Processing helix chain 'E' and resid 133 through 159 removed outlier: 3.528A pdb=" N ILE E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA E 146 " --> pdb=" O TRP E 143 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE E 147 " --> pdb=" O THR E 144 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR E 149 " --> pdb=" O ALA E 146 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS E 150 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL E 155 " --> pdb=" O ILE E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 193 Processing helix chain 'E' and resid 208 through 211 No H-bonds generated for 'chain 'E' and resid 208 through 211' Processing helix chain 'E' and resid 224 through 229 Processing helix chain 'E' and resid 231 through 242 removed outlier: 3.690A pdb=" N ALA E 235 " --> pdb=" O TRP E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 257 No H-bonds generated for 'chain 'E' and resid 255 through 257' Processing helix chain 'E' and resid 259 through 276 Processing helix chain 'E' and resid 284 through 327 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) removed outlier: 3.894A pdb=" N ALA E 315 " --> pdb=" O LEU E 311 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) Proline residue: E 317 - end of helix Processing helix chain 'E' and resid 348 through 351 No H-bonds generated for 'chain 'E' and resid 348 through 351' Processing helix chain 'E' and resid 355 through 400 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) Processing helix chain 'E' and resid 414 through 455 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) Processing helix chain 'E' and resid 459 through 502 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 506 through 511 Processing helix chain 'E' and resid 515 through 564 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 573 through 590 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 593 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 720 through 725 Processing helix chain 'E' and resid 784 through 789 Processing helix chain 'E' and resid 796 through 806 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 809 through 812 No H-bonds generated for 'chain 'E' and resid 809 through 812' Processing helix chain 'E' and resid 818 through 820 No H-bonds generated for 'chain 'E' and resid 818 through 820' Processing helix chain 'E' and resid 832 through 845 removed outlier: 3.615A pdb=" N LEU E 844 " --> pdb=" O VAL E 840 " (cutoff:3.500A) Processing helix chain 'E' and resid 863 through 879 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 918 Processing helix chain 'E' and resid 988 through 992 Processing helix chain 'E' and resid 997 through 1007 removed outlier: 3.614A pdb=" N CYS E1001 " --> pdb=" O PRO E 997 " (cutoff:3.500A) Processing helix chain 'E' and resid 1011 through 1041 removed outlier: 3.597A pdb=" N ASP E1031 " --> pdb=" O LEU E1027 " (cutoff:3.500A) Processing helix chain 'E' and resid 1067 through 1105 Processing helix chain 'E' and resid 1110 through 1115 Processing helix chain 'E' and resid 1120 through 1134 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 1136 through 1160 removed outlier: 4.111A pdb=" N GLU E1141 " --> pdb=" O PRO E1137 " (cutoff:3.500A) Processing helix chain 'E' and resid 1164 through 1209 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 1211 through 1216 Processing helix chain 'E' and resid 1220 through 1272 removed outlier: 3.874A pdb=" N GLY E1256 " --> pdb=" O MET E1252 " (cutoff:3.500A) Processing helix chain 'E' and resid 1279 through 1286 removed outlier: 3.679A pdb=" N LEU E1283 " --> pdb=" O GLY E1279 " (cutoff:3.500A) Processing helix chain 'E' and resid 1291 through 1320 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 1383 through 1392 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) Processing helix chain 'E' and resid 1415 through 1420 Processing helix chain 'E' and resid 1450 through 1458 removed outlier: 3.553A pdb=" N GLU E1456 " --> pdb=" O TRP E1452 " (cutoff:3.500A) Processing helix chain 'E' and resid 1461 through 1466 removed outlier: 3.629A pdb=" N LYS E1465 " --> pdb=" O LYS E1461 " (cutoff:3.500A) Processing helix chain 'E' and resid 1470 through 1472 No H-bonds generated for 'chain 'E' and resid 1470 through 1472' Processing helix chain 'E' and resid 1484 through 1497 removed outlier: 4.412A pdb=" N ARG E1487 " --> pdb=" O GLN E1484 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA E1495 " --> pdb=" O LEU E1492 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE E1496 " --> pdb=" O ALA E1493 " (cutoff:3.500A) Processing helix chain 'E' and resid 1513 through 1528 removed outlier: 3.501A pdb=" N GLU E1517 " --> pdb=" O ASP E1513 " (cutoff:3.500A) Processing helix chain 'E' and resid 1540 through 1544 Processing helix chain 'E' and resid 1565 through 1569 Processing helix chain 'E' and resid 1571 through 1577 Processing sheet with id= A, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= B, first strand: chain 'A' and resid 309 through 311 removed outlier: 6.706A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 234 through 238 removed outlier: 4.143A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 289 " --> pdb=" O THR A 298 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 Processing sheet with id= E, first strand: chain 'B' and resid 181 through 183 Processing sheet with id= F, first strand: chain 'B' and resid 309 through 311 removed outlier: 6.895A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 234 through 238 removed outlier: 4.108A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 313 through 315 Processing sheet with id= I, first strand: chain 'B' and resid 319 through 321 Processing sheet with id= J, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= K, first strand: chain 'C' and resid 309 through 311 removed outlier: 6.636A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 234 through 238 removed outlier: 4.332A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 313 through 315 Processing sheet with id= N, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= O, first strand: chain 'D' and resid 309 through 311 removed outlier: 6.769A pdb=" N ALA D 187 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 234 through 238 removed outlier: 4.135A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (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= Q, first strand: chain 'D' and resid 313 through 315 Processing sheet with id= R, first strand: chain 'D' and resid 319 through 321 Processing sheet with id= S, first strand: chain 'E' and resid 679 through 681 Processing sheet with id= T, first strand: chain 'E' and resid 709 through 713 removed outlier: 6.815A pdb=" N TRP E 899 " --> pdb=" O MET E 710 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL E 712 " --> pdb=" O TRP E 899 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE E 901 " --> pdb=" O VAL E 712 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 850 through 854 removed outlier: 5.367A pdb=" N THR E 883 " --> pdb=" O VAL E 851 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU E 853 " --> pdb=" O THR E 883 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL E 885 " --> pdb=" O LEU E 853 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'E' and resid 1374 through 1376 removed outlier: 5.633A pdb=" N VAL E1533 " --> pdb=" O ILE E1375 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'E' and resid 1422 through 1424 removed outlier: 6.792A pdb=" N ILE E1502 " --> pdb=" O SER E1423 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'E' and resid 685 through 687 removed outlier: 3.752A pdb=" N SER E 734 " --> pdb=" O PHE E 685 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR E 687 " --> pdb=" O LYS E 732 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LYS E 732 " --> pdb=" O THR E 687 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 1549 through 1553 removed outlier: 5.007A pdb=" N LYS E1553 " --> pdb=" O ILE E1557 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE E1557 " --> pdb=" O LYS E1553 " (cutoff:3.500A) 1004 hydrogen bonds defined for protein. 2847 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.56 Time building geometry restraints manager: 9.08 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: 92.67 - 102.13: 91 102.13 - 111.59: 10982 111.59 - 121.04: 12685 121.04 - 130.50: 5697 130.50 - 139.96: 138 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 - 33.21: 12620 33.21 - 66.42: 397 66.42 - 99.63: 71 99.63 - 132.84: 14 132.84 - 166.05: 4 Dihedral angle restraints: 13106 sinusoidal: 5005 harmonic: 8101 Sorted by residual: dihedral pdb=" O16 P5S B 403 " pdb=" C2 P5S B 403 " pdb=" C3 P5S B 403 " pdb=" O37 P5S B 403 " ideal model delta sinusoidal sigma weight residual -57.33 108.72 -166.05 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" O BJX E1602 " pdb=" C16 BJX E1602 " pdb=" C17 BJX E1602 " pdb=" C18 BJX E1602 " ideal model delta sinusoidal sigma weight residual 10.31 -151.38 161.69 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" O16 P5S C 403 " pdb=" C2 P5S C 403 " pdb=" C3 P5S C 403 " pdb=" O37 P5S C 403 " ideal model delta sinusoidal sigma weight residual 302.67 153.95 148.72 1 3.00e+01 1.11e-03 1.98e+01 ... (remaining 13103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2954 0.055 - 0.110: 513 0.110 - 0.166: 55 0.166 - 0.221: 0 0.221 - 0.276: 2 Chirality restraints: 3524 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN E 10 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C5 BJX E1602 " pdb=" C7 BJX E1602 " pdb=" C8 BJX E1602 " pdb=" N1 BJX E1602 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA VAL E 34 " pdb=" N VAL E 34 " pdb=" C VAL E 34 " pdb=" CB VAL E 34 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.15 2.00e-01 2.50e+01 5.31e-01 ... (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: 6191 2.82 - 3.40: 23578 3.40 - 3.98: 38806 3.98 - 4.56: 55393 4.56 - 5.14: 80789 Nonbonded interactions: 204757 Sorted by model distance: nonbonded pdb=" O SER E 541 " pdb=" OG SER E1083 " model vdw 2.235 2.440 nonbonded pdb=" O CYS B 110 " pdb=" OG1 THR B 139 " model vdw 2.242 2.440 nonbonded pdb=" OE1 GLN E 219 " pdb=" NE1 TRP E 232 " model vdw 2.260 2.520 nonbonded pdb=" OD2 ASP B 58 " pdb=" NH1 ARG C 206 " model vdw 2.271 2.520 nonbonded pdb=" O THR E 726 " pdb=" NH2 ARG E 767 " model vdw 2.276 2.520 ... (remaining 204752 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.020 Extract box with map and model: 1.910 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 55.960 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.600 ------------------------------------------------------------------------------- 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 21725 Z= 0.243 Angle : 0.516 10.647 29593 Z= 0.247 Chirality : 0.042 0.276 3524 Planarity : 0.003 0.038 3636 Dihedral : 17.044 166.051 7825 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 *********************** 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 fitting. rotamer outliers: 47 poor density : 588 time to evaluate : 1.930 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: 0.3331 time to fit residues: 318.6674 Evaluate side-chains 544 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 515 time to evaluate : 2.202 ------------------------------------------------------------------------------- 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: 5.9990 chunk 210 optimal weight: 40.0000 chunk 116 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 217 optimal weight: 0.0010 chunk 84 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 chunk 252 optimal weight: 20.0000 overall best weight: 4.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 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 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** E 846 GLN ** E1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1488 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21725 Z= 0.293 Angle : 0.572 9.688 29593 Z= 0.292 Chirality : 0.045 0.296 3524 Planarity : 0.004 0.051 3636 Dihedral : 18.287 165.102 3864 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.85 % Allowed : 11.49 % Favored : 82.66 % 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: 1.28 (0.14), residues: 1345 sheet: -1.42 (0.31), residues: 284 loop : -1.31 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 51 HIS 0.011 0.001 HIS C 193 PHE 0.027 0.002 PHE B 75 TYR 0.023 0.002 TYR D 258 ARG 0.004 0.000 ARG E 598 *********************** 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 646 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 531 time to evaluate : 2.243 Fit side-chains revert: symmetry clash REVERT: A 280 ASP cc_start: 0.7719 (t0) cc_final: 0.7405 (t0) REVERT: B 56 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.6247 (tm) REVERT: B 137 MET cc_start: 0.8975 (mtm) cc_final: 0.8592 (mtm) REVERT: B 186 HIS cc_start: 0.8521 (OUTLIER) cc_final: 0.7272 (p-80) REVERT: B 311 TRP cc_start: 0.8497 (t-100) cc_final: 0.8171 (t60) REVERT: C 163 MET cc_start: 0.8107 (mmp) cc_final: 0.7817 (mmp) REVERT: C 199 MET cc_start: 0.8958 (mtm) cc_final: 0.8394 (mtp) REVERT: C 304 TYR cc_start: 0.9337 (m-80) cc_final: 0.9102 (m-80) REVERT: D 43 ASN cc_start: 0.8502 (t0) cc_final: 0.7352 (t0) REVERT: D 52 GLN cc_start: 0.7765 (mp10) cc_final: 0.7095 (mp10) REVERT: D 325 ARG cc_start: 0.7830 (ptp-170) cc_final: 0.7577 (ptp-170) REVERT: E 299 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8897 (mp) REVERT: E 400 MET cc_start: 0.8288 (mmt) cc_final: 0.8064 (mmt) REVERT: E 1021 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7589 (mm) REVERT: E 1200 LEU cc_start: 0.9434 (tp) cc_final: 0.9207 (tp) REVERT: E 1252 MET cc_start: 0.9039 (mmm) cc_final: 0.8831 (mmt) REVERT: E 1348 GLN cc_start: 0.6829 (OUTLIER) cc_final: 0.6474 (pp30) outliers start: 115 outliers final: 76 residues processed: 587 average time/residue: 0.3285 time to fit residues: 299.2418 Evaluate side-chains 585 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 504 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 107 ASN 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 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 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 124 SER Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 190 THR 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 58 ASP Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 190 THR 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 71 THR Chi-restraints excluded: chain D residue 99 ASP 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 1 MET Chi-restraints excluded: chain E residue 18 ASP 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 209 ASP 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 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 404 THR 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 587 VAL Chi-restraints excluded: chain E residue 861 ASP Chi-restraints excluded: chain E residue 1015 LEU Chi-restraints excluded: chain E residue 1021 LEU Chi-restraints excluded: chain E residue 1083 SER 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 140 optimal weight: 40.0000 chunk 78 optimal weight: 0.8980 chunk 210 optimal weight: 40.0000 chunk 171 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 252 optimal weight: 30.0000 chunk 273 optimal weight: 0.8980 chunk 225 optimal weight: 10.0000 chunk 250 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 202 optimal weight: 30.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN C 313 GLN D 235 GLN E 326 HIS E 500 ASN ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1020 GLN ** E1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21725 Z= 0.283 Angle : 0.566 9.624 29593 Z= 0.285 Chirality : 0.045 0.299 3524 Planarity : 0.004 0.038 3636 Dihedral : 17.520 164.745 3854 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 6.76 % Allowed : 12.81 % Favored : 80.43 % 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: -0.06 (0.16), residues: 2770 helix: 1.28 (0.14), residues: 1347 sheet: -1.21 (0.32), residues: 272 loop : -1.33 (0.18), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 91 HIS 0.018 0.001 HIS B 278 PHE 0.036 0.002 PHE B 75 TYR 0.026 0.002 TYR D 258 ARG 0.003 0.000 ARG E 16 *********************** 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 648 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 515 time to evaluate : 2.139 Fit side-chains revert: symmetry clash REVERT: A 205 LEU cc_start: 0.8750 (mt) cc_final: 0.8504 (mt) REVERT: B 137 MET cc_start: 0.8993 (mtm) cc_final: 0.8614 (mtm) REVERT: B 186 HIS cc_start: 0.8564 (OUTLIER) cc_final: 0.7430 (p-80) REVERT: B 217 MET cc_start: 0.9128 (mtp) cc_final: 0.8920 (mtp) REVERT: B 311 TRP cc_start: 0.8513 (t-100) cc_final: 0.8172 (t60) REVERT: C 163 MET cc_start: 0.8082 (mmp) cc_final: 0.7847 (mmp) REVERT: C 195 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6750 (mmm160) REVERT: C 199 MET cc_start: 0.8947 (mtm) cc_final: 0.8696 (mtp) REVERT: C 304 TYR cc_start: 0.9307 (m-80) cc_final: 0.9029 (m-80) REVERT: D 43 ASN cc_start: 0.8480 (t0) cc_final: 0.7372 (t0) REVERT: D 52 GLN cc_start: 0.7702 (mp10) cc_final: 0.7058 (mp10) REVERT: D 80 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9023 (mp) REVERT: D 325 ARG cc_start: 0.7832 (ptp-170) cc_final: 0.7557 (ptp-170) REVERT: E 16 ARG cc_start: 0.8548 (tpp80) cc_final: 0.8272 (tpp80) REVERT: E 253 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8391 (tp) REVERT: E 299 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8835 (mp) REVERT: E 400 MET cc_start: 0.8263 (mmt) cc_final: 0.7957 (mmt) REVERT: E 781 ASN cc_start: 0.7734 (p0) cc_final: 0.7294 (p0) REVERT: E 785 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7353 (tm-30) REVERT: E 1021 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7574 (mm) REVERT: E 1227 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8810 (tp) REVERT: E 1348 GLN cc_start: 0.6689 (OUTLIER) cc_final: 0.6324 (pp30) outliers start: 133 outliers final: 97 residues processed: 584 average time/residue: 0.3108 time to fit residues: 283.9976 Evaluate side-chains 601 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 496 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 107 ASN 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 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 124 SER Chi-restraints excluded: chain B residue 139 THR 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 278 HIS 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 58 ASP 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 195 ARG Chi-restraints excluded: chain C residue 202 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 71 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 99 ASP 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 341 THR Chi-restraints excluded: chain E residue 1 MET 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 209 ASP 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 404 THR 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 861 ASP 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 1227 LEU 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 249 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 169 optimal weight: 0.0870 chunk 253 optimal weight: 4.9990 chunk 268 optimal weight: 40.0000 chunk 132 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 GLN C 313 GLN C 335 ASN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 HIS D 235 GLN E 326 HIS ** E1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1308 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21725 Z= 0.226 Angle : 0.539 9.750 29593 Z= 0.269 Chirality : 0.044 0.293 3524 Planarity : 0.004 0.043 3636 Dihedral : 16.868 164.502 3850 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 6.76 % Allowed : 14.23 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.42 (0.14), residues: 1349 sheet: -1.19 (0.32), residues: 272 loop : -1.31 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 91 HIS 0.010 0.001 HIS C 193 PHE 0.039 0.002 PHE B 75 TYR 0.026 0.001 TYR D 258 ARG 0.007 0.000 ARG E1145 *********************** 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 652 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 519 time to evaluate : 2.190 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8391 (pt) REVERT: B 72 LEU cc_start: 0.8472 (mm) cc_final: 0.8163 (mm) REVERT: B 137 MET cc_start: 0.8951 (mtm) cc_final: 0.8572 (mtm) REVERT: B 186 HIS cc_start: 0.8557 (OUTLIER) cc_final: 0.7493 (p-80) REVERT: B 240 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8053 (ttt) REVERT: B 311 TRP cc_start: 0.8527 (t-100) cc_final: 0.8210 (t60) REVERT: B 347 ARG cc_start: 0.8193 (ttm170) cc_final: 0.7956 (ttm170) REVERT: C 128 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: C 163 MET cc_start: 0.8053 (mmp) cc_final: 0.7787 (mmp) REVERT: C 195 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6794 (ttm110) REVERT: C 199 MET cc_start: 0.8873 (mtm) cc_final: 0.8665 (mtp) REVERT: C 304 TYR cc_start: 0.9248 (m-80) cc_final: 0.8939 (m-80) REVERT: D 43 ASN cc_start: 0.8472 (t0) cc_final: 0.7317 (t0) REVERT: D 52 GLN cc_start: 0.7675 (mp10) cc_final: 0.7014 (mp10) REVERT: D 80 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9074 (mp) REVERT: D 206 ARG cc_start: 0.7913 (mmt90) cc_final: 0.7564 (mmt90) REVERT: D 325 ARG cc_start: 0.7811 (ptp-170) cc_final: 0.7536 (ptp-170) REVERT: E 16 ARG cc_start: 0.8528 (tpp80) cc_final: 0.8263 (tpp80) REVERT: E 264 GLN cc_start: 0.8302 (mt0) cc_final: 0.7890 (mt0) REVERT: E 299 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8814 (mp) REVERT: E 312 LEU cc_start: 0.9138 (mt) cc_final: 0.8926 (mt) REVERT: E 781 ASN cc_start: 0.7734 (p0) cc_final: 0.7274 (p0) REVERT: E 785 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7287 (tm-30) REVERT: E 1021 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7609 (mm) REVERT: E 1197 GLN cc_start: 0.8336 (pp30) cc_final: 0.8099 (pp30) REVERT: E 1227 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8781 (tp) REVERT: E 1348 GLN cc_start: 0.6726 (OUTLIER) cc_final: 0.6375 (pp30) outliers start: 133 outliers final: 101 residues processed: 584 average time/residue: 0.3366 time to fit residues: 305.2715 Evaluate side-chains 609 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 498 time to evaluate : 2.733 ------------------------------------------------------------------------------- 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 107 ASN 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 137 MET Chi-restraints excluded: chain A residue 139 THR 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 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 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 124 SER Chi-restraints excluded: chain B residue 139 THR 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 240 MET 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 58 ASP Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 128 GLN 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 195 ARG Chi-restraints excluded: chain C residue 202 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 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 341 THR Chi-restraints excluded: chain D residue 345 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 152 ILE 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 241 HIS 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 404 THR 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 538 VAL 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 861 ASP 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 1071 LEU Chi-restraints excluded: chain E residue 1083 SER Chi-restraints excluded: chain E residue 1146 SER Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1248 LEU 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 223 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 200 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 229 optimal weight: 20.0000 chunk 185 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 137 optimal weight: 3.9990 chunk 241 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN B 247 ASN B 278 HIS C 128 GLN C 313 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN D 234 HIS E 326 HIS ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1020 GLN ** E1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1224 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21725 Z= 0.363 Angle : 0.609 10.407 29593 Z= 0.304 Chirality : 0.046 0.303 3524 Planarity : 0.004 0.038 3636 Dihedral : 16.749 164.534 3850 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 7.63 % Allowed : 14.90 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.13 (0.16), residues: 2770 helix: 1.23 (0.14), residues: 1353 sheet: -1.26 (0.32), residues: 272 loop : -1.40 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 91 HIS 0.010 0.001 HIS C 193 PHE 0.034 0.002 PHE B 75 TYR 0.028 0.002 TYR D 258 ARG 0.009 0.001 ARG A 314 *********************** 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 652 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 502 time to evaluate : 2.304 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8461 (pt) REVERT: A 205 LEU cc_start: 0.8777 (mt) cc_final: 0.8553 (mt) REVERT: B 137 MET cc_start: 0.9017 (mtm) cc_final: 0.8632 (mtm) REVERT: B 186 HIS cc_start: 0.8712 (OUTLIER) cc_final: 0.7577 (p-80) REVERT: B 311 TRP cc_start: 0.8597 (t-100) cc_final: 0.8208 (t60) REVERT: C 47 LYS cc_start: 0.8608 (mttp) cc_final: 0.8392 (mttm) REVERT: C 128 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8379 (tt0) REVERT: C 163 MET cc_start: 0.8084 (mmp) cc_final: 0.7839 (mmp) REVERT: C 195 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6886 (mmm160) REVERT: C 199 MET cc_start: 0.8936 (mtm) cc_final: 0.8665 (mtp) REVERT: D 43 ASN cc_start: 0.8504 (t0) cc_final: 0.7446 (t0) REVERT: D 80 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9130 (mp) REVERT: D 206 ARG cc_start: 0.7879 (mmt90) cc_final: 0.7542 (mmt90) REVERT: E 16 ARG cc_start: 0.8548 (tpp80) cc_final: 0.8272 (tpp80) REVERT: E 253 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8402 (tp) REVERT: E 264 GLN cc_start: 0.8335 (mt0) cc_final: 0.7974 (mt0) REVERT: E 299 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8852 (mp) REVERT: E 312 LEU cc_start: 0.9199 (mt) cc_final: 0.8995 (mt) REVERT: E 598 ARG cc_start: 0.8770 (ttm110) cc_final: 0.8466 (mtp85) REVERT: E 781 ASN cc_start: 0.7859 (p0) cc_final: 0.7393 (p0) REVERT: E 1021 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7544 (mm) REVERT: E 1197 GLN cc_start: 0.8521 (pp30) cc_final: 0.8220 (pp30) REVERT: E 1227 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8886 (tp) REVERT: E 1348 GLN cc_start: 0.6694 (OUTLIER) cc_final: 0.6324 (pp30) outliers start: 150 outliers final: 122 residues processed: 581 average time/residue: 0.3359 time to fit residues: 303.2364 Evaluate side-chains 630 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 498 time to evaluate : 2.078 ------------------------------------------------------------------------------- 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 107 ASN 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 137 MET Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 184 SER 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 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 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 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 108 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 139 THR 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 278 HIS 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 343 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 58 ASP 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 128 GLN 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 195 ARG 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 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 99 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 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 319 VAL Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 1 MET 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 152 ILE 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 223 ASN Chi-restraints excluded: chain E residue 241 HIS 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 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 404 THR 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 543 SER 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 821 THR Chi-restraints excluded: chain E residue 861 ASP 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 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 1146 SER Chi-restraints excluded: chain E residue 1161 THR Chi-restraints excluded: chain E residue 1220 GLU Chi-restraints excluded: chain E residue 1227 LEU 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 90 optimal weight: 20.0000 chunk 241 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 268 optimal weight: 40.0000 chunk 223 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 HIS B 278 HIS C 128 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 21725 Z= 0.450 Angle : 0.652 10.750 29593 Z= 0.328 Chirality : 0.048 0.314 3524 Planarity : 0.004 0.039 3636 Dihedral : 16.787 164.239 3850 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 8.34 % Allowed : 15.46 % 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: -0.40 (0.16), residues: 2770 helix: 0.98 (0.14), residues: 1360 sheet: -1.42 (0.31), residues: 278 loop : -1.48 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 91 HIS 0.019 0.001 HIS B 278 PHE 0.033 0.002 PHE B 75 TYR 0.029 0.002 TYR D 258 ARG 0.006 0.001 ARG A 206 *********************** 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 672 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 508 time to evaluate : 2.745 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8546 (pt) REVERT: A 205 LEU cc_start: 0.8778 (mt) cc_final: 0.8560 (mt) REVERT: B 137 MET cc_start: 0.9043 (mtm) cc_final: 0.8662 (mtm) REVERT: B 186 HIS cc_start: 0.8791 (OUTLIER) cc_final: 0.7647 (p-80) REVERT: B 311 TRP cc_start: 0.8589 (t-100) cc_final: 0.8178 (t60) REVERT: C 128 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8475 (tt0) REVERT: C 163 MET cc_start: 0.8101 (mmp) cc_final: 0.7891 (mmp) REVERT: C 199 MET cc_start: 0.8954 (mtm) cc_final: 0.8547 (mtp) REVERT: D 43 ASN cc_start: 0.8517 (t0) cc_final: 0.7416 (t0) REVERT: D 80 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9147 (mp) REVERT: D 206 ARG cc_start: 0.8017 (mmt90) cc_final: 0.7702 (mmt90) REVERT: E 253 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8357 (tp) REVERT: E 264 GLN cc_start: 0.8347 (mt0) cc_final: 0.7972 (mt0) REVERT: E 299 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8868 (mp) REVERT: E 312 LEU cc_start: 0.9224 (mt) cc_final: 0.9018 (mt) REVERT: E 781 ASN cc_start: 0.7937 (p0) cc_final: 0.7490 (p0) REVERT: E 1021 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7574 (mm) REVERT: E 1197 GLN cc_start: 0.8581 (pp30) cc_final: 0.8250 (pp30) REVERT: E 1272 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7235 (mp) REVERT: E 1348 GLN cc_start: 0.6620 (OUTLIER) cc_final: 0.6169 (pp30) outliers start: 164 outliers final: 136 residues processed: 595 average time/residue: 0.3273 time to fit residues: 302.6703 Evaluate side-chains 644 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 499 time to evaluate : 2.373 ------------------------------------------------------------------------------- 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 107 ASN 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 137 MET Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 184 SER 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 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 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 341 THR Chi-restraints excluded: chain A residue 343 LEU 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 124 SER Chi-restraints excluded: chain B residue 139 THR 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 278 HIS 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 343 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 58 ASP 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 128 GLN 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 195 ARG 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 298 THR 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 99 ASP 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 186 HIS Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 236 VAL 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 280 ASP 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 D residue 345 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 152 ILE 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 223 ASN Chi-restraints excluded: chain E residue 241 HIS 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 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 417 ILE 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 543 SER 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 726 THR Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 846 GLN Chi-restraints excluded: chain E residue 848 THR Chi-restraints excluded: chain E residue 861 ASP 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 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 1146 SER Chi-restraints excluded: chain E residue 1161 THR 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 1272 LEU 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 259 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 226 optimal weight: 40.0000 chunk 150 optimal weight: 3.9990 chunk 267 optimal weight: 0.3980 chunk 167 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 278 HIS C 128 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 326 HIS ** E 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1308 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21725 Z= 0.264 Angle : 0.576 11.935 29593 Z= 0.286 Chirality : 0.045 0.290 3524 Planarity : 0.004 0.044 3636 Dihedral : 16.473 163.480 3850 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 7.78 % Allowed : 16.12 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.21 (0.14), residues: 1360 sheet: -1.54 (0.30), residues: 281 loop : -1.37 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E1247 HIS 0.021 0.001 HIS B 278 PHE 0.026 0.002 PHE A 168 TYR 0.025 0.002 TYR D 258 ARG 0.006 0.000 ARG A 206 *********************** 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 666 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 513 time to evaluate : 2.491 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8483 (pt) REVERT: A 347 ARG cc_start: 0.8297 (tpp80) cc_final: 0.8053 (tpp80) REVERT: B 137 MET cc_start: 0.8989 (mtm) cc_final: 0.8602 (mtm) REVERT: B 186 HIS cc_start: 0.8731 (OUTLIER) cc_final: 0.7575 (p-80) REVERT: B 240 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8012 (ttt) REVERT: B 311 TRP cc_start: 0.8563 (t-100) cc_final: 0.8184 (t60) REVERT: C 128 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8464 (tt0) REVERT: C 163 MET cc_start: 0.8066 (mmp) cc_final: 0.7860 (mmp) REVERT: C 199 MET cc_start: 0.8913 (mtm) cc_final: 0.8665 (mtp) REVERT: D 43 ASN cc_start: 0.8489 (t0) cc_final: 0.7492 (t0) REVERT: D 80 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9123 (mp) REVERT: D 206 ARG cc_start: 0.7956 (mmt90) cc_final: 0.7648 (mmt90) REVERT: E 16 ARG cc_start: 0.8573 (tpp80) cc_final: 0.8331 (tpp80) REVERT: E 299 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8801 (mp) REVERT: E 598 ARG cc_start: 0.8800 (ttm110) cc_final: 0.8472 (mtp85) REVERT: E 781 ASN cc_start: 0.7868 (p0) cc_final: 0.7396 (p0) REVERT: E 785 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7219 (tm-30) REVERT: E 1021 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7623 (mm) REVERT: E 1197 GLN cc_start: 0.8504 (pp30) cc_final: 0.8184 (pp30) REVERT: E 1272 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7333 (mp) REVERT: E 1348 GLN cc_start: 0.6681 (OUTLIER) cc_final: 0.6380 (pp30) outliers start: 153 outliers final: 128 residues processed: 593 average time/residue: 0.3273 time to fit residues: 303.0250 Evaluate side-chains 635 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 498 time to evaluate : 2.260 ------------------------------------------------------------------------------- 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 107 ASN 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 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 223 THR 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 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 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 108 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 139 THR 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 240 MET 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 292 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 36 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 58 ASP 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 128 GLN 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 195 ARG 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 345 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 99 ASP 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 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 319 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 44 PHE 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 209 ASP Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 241 HIS Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 260 LEU 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 404 THR Chi-restraints excluded: chain E residue 417 ILE 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 543 SER Chi-restraints excluded: chain E residue 557 ILE Chi-restraints excluded: chain E residue 709 THR Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 848 THR Chi-restraints excluded: chain E residue 861 ASP 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 1026 VAL 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 1146 SER Chi-restraints excluded: chain E residue 1161 THR 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 1272 LEU 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 165 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 210 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 278 HIS C 128 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21725 Z= 0.335 Angle : 0.605 12.198 29593 Z= 0.301 Chirality : 0.046 0.302 3524 Planarity : 0.004 0.039 3636 Dihedral : 16.386 163.727 3848 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 7.83 % Allowed : 16.12 % Favored : 76.05 % 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: 1.18 (0.14), residues: 1354 sheet: -1.56 (0.30), residues: 276 loop : -1.39 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E1247 HIS 0.021 0.001 HIS B 278 PHE 0.025 0.002 PHE C 75 TYR 0.026 0.002 TYR D 258 ARG 0.007 0.001 ARG A 206 *********************** 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 663 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 509 time to evaluate : 2.312 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8515 (pt) REVERT: A 347 ARG cc_start: 0.8297 (tpp80) cc_final: 0.8053 (tpp80) REVERT: B 137 MET cc_start: 0.9005 (mtm) cc_final: 0.8613 (mtm) REVERT: B 186 HIS cc_start: 0.8778 (OUTLIER) cc_final: 0.7660 (p-80) REVERT: B 240 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8017 (ttt) REVERT: B 311 TRP cc_start: 0.8577 (t-100) cc_final: 0.8188 (t60) REVERT: C 128 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8461 (tt0) REVERT: C 199 MET cc_start: 0.8953 (mtm) cc_final: 0.8543 (mtp) REVERT: D 43 ASN cc_start: 0.8487 (t0) cc_final: 0.7425 (t0) REVERT: D 80 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9125 (mp) REVERT: D 206 ARG cc_start: 0.8012 (mmt90) cc_final: 0.7672 (mmt90) REVERT: E 16 ARG cc_start: 0.8559 (tpp80) cc_final: 0.8294 (tpp80) REVERT: E 264 GLN cc_start: 0.8266 (mt0) cc_final: 0.7857 (mt0) REVERT: E 299 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8817 (mp) REVERT: E 312 LEU cc_start: 0.9224 (mt) cc_final: 0.8944 (mp) REVERT: E 598 ARG cc_start: 0.8823 (ttm110) cc_final: 0.8486 (mtp85) REVERT: E 781 ASN cc_start: 0.7876 (p0) cc_final: 0.7433 (p0) REVERT: E 785 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7231 (tm-30) REVERT: E 1021 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7622 (mm) REVERT: E 1197 GLN cc_start: 0.8542 (pp30) cc_final: 0.8214 (pp30) REVERT: E 1272 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7323 (mp) REVERT: E 1348 GLN cc_start: 0.6644 (OUTLIER) cc_final: 0.6371 (pp30) outliers start: 154 outliers final: 131 residues processed: 587 average time/residue: 0.3362 time to fit residues: 307.1926 Evaluate side-chains 643 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 503 time to evaluate : 2.278 ------------------------------------------------------------------------------- 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 107 ASN 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 137 MET Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 184 SER 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 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 325 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 343 LEU 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 124 SER Chi-restraints excluded: chain B residue 139 THR 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 233 LEU Chi-restraints excluded: chain B residue 240 MET 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 343 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 58 ASP 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 128 GLN 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 195 ARG 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 298 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER 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 99 ASP 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 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 280 ASP 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 D residue 345 THR Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 44 PHE 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 209 ASP Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 241 HIS Chi-restraints excluded: chain E residue 260 LEU 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 404 THR Chi-restraints excluded: chain E residue 417 ILE 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 543 SER 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 726 THR Chi-restraints excluded: chain E residue 846 GLN Chi-restraints excluded: chain E residue 848 THR Chi-restraints excluded: chain E residue 861 ASP 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 1026 VAL 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 1146 SER Chi-restraints excluded: chain E residue 1161 THR 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 1272 LEU 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 243 optimal weight: 0.9990 chunk 256 optimal weight: 50.0000 chunk 234 optimal weight: 9.9990 chunk 249 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 196 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 225 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21725 Z= 0.269 Angle : 0.579 11.779 29593 Z= 0.285 Chirality : 0.045 0.290 3524 Planarity : 0.004 0.040 3636 Dihedral : 16.161 163.557 3848 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 7.68 % Allowed : 16.73 % 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: -0.08 (0.16), residues: 2770 helix: 1.31 (0.14), residues: 1348 sheet: -1.63 (0.30), residues: 286 loop : -1.30 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E1247 HIS 0.008 0.001 HIS C 193 PHE 0.025 0.002 PHE C 75 TYR 0.026 0.002 TYR D 258 ARG 0.007 0.000 ARG A 206 *********************** 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 662 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 511 time to evaluate : 2.335 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8499 (pt) REVERT: A 314 ARG cc_start: 0.8137 (ttp-110) cc_final: 0.7782 (ttm110) REVERT: A 325 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7432 (ptp-110) REVERT: A 347 ARG cc_start: 0.8299 (tpp80) cc_final: 0.8050 (tpp80) REVERT: B 137 MET cc_start: 0.8968 (mtm) cc_final: 0.8581 (mtm) REVERT: B 186 HIS cc_start: 0.8739 (OUTLIER) cc_final: 0.7583 (p-80) REVERT: B 192 ARG cc_start: 0.7175 (mtp85) cc_final: 0.6962 (mtp85) REVERT: B 240 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8027 (ttt) REVERT: B 311 TRP cc_start: 0.8558 (t-100) cc_final: 0.8175 (t60) REVERT: C 199 MET cc_start: 0.8918 (mtm) cc_final: 0.8521 (mtp) REVERT: D 43 ASN cc_start: 0.8540 (t0) cc_final: 0.7558 (t0) REVERT: D 80 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9120 (mp) REVERT: D 206 ARG cc_start: 0.8036 (mmt90) cc_final: 0.7722 (mmt90) REVERT: E 16 ARG cc_start: 0.8527 (tpp80) cc_final: 0.8256 (tpp80) REVERT: E 252 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8616 (ptmt) REVERT: E 264 GLN cc_start: 0.8238 (mt0) cc_final: 0.7863 (mt0) REVERT: E 299 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8783 (mp) REVERT: E 312 LEU cc_start: 0.9217 (mt) cc_final: 0.8946 (mp) REVERT: E 506 MET cc_start: 0.7009 (tpt) cc_final: 0.6340 (tpp) REVERT: E 598 ARG cc_start: 0.8783 (ttm110) cc_final: 0.8471 (mtp85) REVERT: E 781 ASN cc_start: 0.7857 (p0) cc_final: 0.7404 (p0) REVERT: E 785 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7213 (tm-30) REVERT: E 1021 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7664 (mm) REVERT: E 1197 GLN cc_start: 0.8491 (pp30) cc_final: 0.8157 (pp30) REVERT: E 1272 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7303 (mp) REVERT: E 1348 GLN cc_start: 0.6650 (OUTLIER) cc_final: 0.6393 (pp30) outliers start: 151 outliers final: 129 residues processed: 591 average time/residue: 0.3546 time to fit residues: 326.9832 Evaluate side-chains 649 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 510 time to evaluate : 2.630 ------------------------------------------------------------------------------- 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 107 ASN 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 137 MET Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 184 SER 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 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 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 108 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 139 THR 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 233 LEU Chi-restraints excluded: chain B residue 240 MET 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 36 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 58 ASP 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 195 ARG 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 298 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER 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 99 ASP 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 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 280 ASP 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 D residue 345 THR Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 44 PHE 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 209 ASP Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 241 HIS Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 260 LEU 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 404 THR Chi-restraints excluded: chain E residue 417 ILE 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 543 SER 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 726 THR Chi-restraints excluded: chain E residue 846 GLN Chi-restraints excluded: chain E residue 848 THR Chi-restraints excluded: chain E residue 861 ASP 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 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 1146 SER Chi-restraints excluded: chain E residue 1152 SER Chi-restraints excluded: chain E residue 1161 THR 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 1272 LEU 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 163 optimal weight: 2.9990 chunk 264 optimal weight: 0.6980 chunk 161 optimal weight: 10.0000 chunk 125 optimal weight: 0.6980 chunk 183 optimal weight: 6.9990 chunk 276 optimal weight: 10.0000 chunk 254 optimal weight: 9.9990 chunk 220 optimal weight: 50.0000 chunk 22 optimal weight: 30.0000 chunk 170 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21725 Z= 0.272 Angle : 0.581 11.613 29593 Z= 0.285 Chirality : 0.045 0.289 3524 Planarity : 0.004 0.039 3636 Dihedral : 15.876 163.903 3848 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 7.57 % Allowed : 16.93 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.35 (0.14), residues: 1350 sheet: -1.53 (0.30), residues: 276 loop : -1.30 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 91 HIS 0.008 0.001 HIS C 193 PHE 0.024 0.002 PHE C 75 TYR 0.028 0.002 TYR D 258 ARG 0.008 0.000 ARG A 206 ********************** 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 657 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 508 time to evaluate : 2.229 Fit side-chains revert: symmetry clash REVERT: A 2 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8504 (pt) REVERT: A 332 LYS cc_start: 0.8913 (mttt) cc_final: 0.8674 (mtmt) REVERT: A 347 ARG cc_start: 0.8302 (tpp80) cc_final: 0.8052 (tpp80) REVERT: B 137 MET cc_start: 0.8959 (mtm) cc_final: 0.8575 (mtm) REVERT: B 186 HIS cc_start: 0.8750 (OUTLIER) cc_final: 0.7595 (p-80) REVERT: B 192 ARG cc_start: 0.7113 (mtp85) cc_final: 0.6902 (mtp85) REVERT: B 240 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8037 (ttt) REVERT: B 311 TRP cc_start: 0.8559 (t-100) cc_final: 0.8184 (t60) REVERT: B 314 ARG cc_start: 0.7619 (mtt180) cc_final: 0.7356 (mtt90) REVERT: C 128 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8411 (tt0) REVERT: C 199 MET cc_start: 0.8919 (mtm) cc_final: 0.8518 (mtp) REVERT: D 43 ASN cc_start: 0.8506 (t0) cc_final: 0.7483 (t0) REVERT: D 80 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9114 (mp) REVERT: D 191 LEU cc_start: 0.8284 (tt) cc_final: 0.8017 (tp) REVERT: D 206 ARG cc_start: 0.8027 (mmt90) cc_final: 0.7703 (mmt90) REVERT: E 16 ARG cc_start: 0.8538 (tpp80) cc_final: 0.8263 (tpp80) REVERT: E 184 LEU cc_start: 0.8727 (mt) cc_final: 0.8524 (mt) REVERT: E 252 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8627 (ptmt) REVERT: E 264 GLN cc_start: 0.8239 (mt0) cc_final: 0.7865 (mt0) REVERT: E 299 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8768 (mp) REVERT: E 312 LEU cc_start: 0.9228 (mt) cc_final: 0.8966 (mp) REVERT: E 598 ARG cc_start: 0.8760 (ttm110) cc_final: 0.8464 (mtp85) REVERT: E 781 ASN cc_start: 0.7856 (p0) cc_final: 0.7424 (p0) REVERT: E 1021 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7624 (mm) REVERT: E 1197 GLN cc_start: 0.8482 (pp30) cc_final: 0.8125 (pp30) REVERT: E 1272 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7297 (mp) REVERT: E 1348 GLN cc_start: 0.6695 (OUTLIER) cc_final: 0.6458 (pp30) outliers start: 149 outliers final: 128 residues processed: 585 average time/residue: 0.3550 time to fit residues: 322.7399 Evaluate side-chains 639 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 501 time to evaluate : 2.344 ------------------------------------------------------------------------------- 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 107 ASN 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 137 MET Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 184 SER 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 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 325 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 343 LEU 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 124 SER Chi-restraints excluded: chain B residue 139 THR 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 233 LEU Chi-restraints excluded: chain B residue 240 MET 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 36 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 58 ASP 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 128 GLN 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 298 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 37 SER 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 99 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 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 255 LEU Chi-restraints excluded: chain D residue 264 ASN Chi-restraints excluded: chain D residue 280 ASP 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 D residue 345 THR Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 44 PHE 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 209 ASP Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 241 HIS Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 260 LEU 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 404 THR Chi-restraints excluded: chain E residue 417 ILE 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 543 SER 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 726 THR Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 846 GLN Chi-restraints excluded: chain E residue 848 THR Chi-restraints excluded: chain E residue 861 ASP 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 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 1146 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 1272 LEU 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 175 optimal weight: 0.0570 chunk 234 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 203 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 220 optimal weight: 50.0000 chunk 92 optimal weight: 0.5980 chunk 226 optimal weight: 0.6980 chunk 27 optimal weight: 20.0000 chunk 40 optimal weight: 0.7980 overall best weight: 1.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 326 HIS ** E1123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.179254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.152191 restraints weight = 25576.789| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.88 r_work: 0.3502 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21725 Z= 0.168 Angle : 0.549 10.896 29593 Z= 0.267 Chirality : 0.043 0.270 3524 Planarity : 0.004 0.038 3636 Dihedral : 15.557 163.921 3848 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.39 % Allowed : 19.37 % Favored : 75.24 % 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: 0.24 (0.17), residues: 2770 helix: 1.59 (0.15), residues: 1342 sheet: -1.55 (0.30), residues: 286 loop : -1.12 (0.19), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E1247 HIS 0.009 0.001 HIS C 193 PHE 0.027 0.001 PHE B 75 TYR 0.028 0.001 TYR B 304 ARG 0.007 0.000 ARG A 206 =============================================================================== Job complete usr+sys time: 5956.07 seconds wall clock time: 109 minutes 40.47 seconds (6580.47 seconds total)