Starting phenix.real_space_refine on Sun Feb 18 15:36:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xho_33197/02_2024/7xho_33197.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xho_33197/02_2024/7xho_33197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xho_33197/02_2024/7xho_33197.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xho_33197/02_2024/7xho_33197.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xho_33197/02_2024/7xho_33197.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xho_33197/02_2024/7xho_33197.pdb" } resolution = 3.29 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 187 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 14198 2.51 5 N 3821 2.21 5 O 4108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 66": "OE1" <-> "OE2" Residue "H GLU 83": "OE1" <-> "OE2" Residue "H GLU 97": "OE1" <-> "OE2" Residue "H GLU 152": "OE1" <-> "OE2" Residue "I GLU 96": "OE1" <-> "OE2" Residue "I GLU 566": "OE1" <-> "OE2" Residue "K GLU 27": "OE1" <-> "OE2" Residue "K GLU 30": "OE1" <-> "OE2" Residue "L GLU 57": "OE1" <-> "OE2" Residue "L GLU 190": "OE1" <-> "OE2" Residue "L PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 259": "OE1" <-> "OE2" Residue "L GLU 278": "OE1" <-> "OE2" Residue "M GLU 38": "OE1" <-> "OE2" Residue "M GLU 43": "OE1" <-> "OE2" Residue "M TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 134": "OE1" <-> "OE2" Residue "M GLU 136": "OE1" <-> "OE2" Residue "N GLU 20": "OE1" <-> "OE2" Residue "N GLU 33": "OE1" <-> "OE2" Residue "O GLU 258": "OE1" <-> "OE2" Residue "O GLU 265": "OE1" <-> "OE2" Residue "O GLU 266": "OE1" <-> "OE2" Residue "P GLU 64": "OE1" <-> "OE2" Residue "P GLU 143": "OE1" <-> "OE2" Residue "P GLU 159": "OE1" <-> "OE2" Residue "S GLU 52": "OE1" <-> "OE2" Residue "T GLU 476": "OE1" <-> "OE2" Residue "T GLU 484": "OE1" <-> "OE2" Residue "T GLU 499": "OE1" <-> "OE2" Residue "T GLU 513": "OE1" <-> "OE2" Residue "T GLU 536": "OE1" <-> "OE2" Residue "T GLU 542": "OE1" <-> "OE2" Residue "W GLU 36": "OE1" <-> "OE2" Residue "W GLU 56": "OE1" <-> "OE2" Residue "W GLU 57": "OE1" <-> "OE2" Residue "W GLU 73": "OE1" <-> "OE2" Residue "X GLU 48": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22243 Number of models: 1 Model: "" Number of chains: 17 Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 40 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1560 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "I" Number of atoms: 4111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4111 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 15, 'TRANS': 501} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "K" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1869 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "L" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2422 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 288} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1298 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 7, 'TRANS': 160} Chain: "N" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2492 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 290} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "O" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1588 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 196} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "P" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1808 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "Q" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1175 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 57 Chain: "S" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 790 Classifications: {'peptide': 97} Link IDs: {'TRANS': 96} Chain: "T" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 804 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "W" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 584 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "X" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 590 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "c" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 308 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'TRANS': 61} Chain breaks: 1 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 90 Chain: "U" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 699 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 479 Unresolved non-hydrogen angles: 594 Unresolved non-hydrogen dihedrals: 398 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 14, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 250 Time building chain proxies: 11.89, per 1000 atoms: 0.53 Number of scatterers: 22243 At special positions: 0 Unit cell: (107.36, 169.58, 186.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 116 16.00 O 4108 8.00 N 3821 7.00 C 14198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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 Time building additional restraints: 8.75 Conformation dependent library (CDL) restraints added in 4.2 seconds 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5586 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 12 sheets defined 64.0% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'H' and resid 40 through 66 removed outlier: 3.684A pdb=" N GLN H 52 " --> pdb=" O ALA H 48 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU H 55 " --> pdb=" O LYS H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 82 removed outlier: 3.656A pdb=" N ILE H 82 " --> pdb=" O ILE H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 87 Processing helix chain 'H' and resid 87 through 116 removed outlier: 3.811A pdb=" N LYS H 93 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS H 99 " --> pdb=" O ALA H 95 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS H 100 " --> pdb=" O PHE H 96 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR H 110 " --> pdb=" O MET H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 188 removed outlier: 3.675A pdb=" N GLU H 146 " --> pdb=" O LYS H 142 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER H 147 " --> pdb=" O SER H 143 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU H 152 " --> pdb=" O TRP H 148 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP H 185 " --> pdb=" O LYS H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 210 removed outlier: 3.569A pdb=" N ILE H 198 " --> pdb=" O ARG H 194 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS H 207 " --> pdb=" O GLN H 203 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE H 208 " --> pdb=" O MET H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 237 removed outlier: 3.858A pdb=" N GLU H 235 " --> pdb=" O PRO H 231 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE H 236 " --> pdb=" O ALA H 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 75 Processing helix chain 'I' and resid 84 through 99 removed outlier: 4.301A pdb=" N LEU I 88 " --> pdb=" O LYS I 84 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU I 89 " --> pdb=" O ASP I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 112 Processing helix chain 'I' and resid 122 through 131 removed outlier: 4.171A pdb=" N LEU I 130 " --> pdb=" O ASN I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 147 removed outlier: 3.761A pdb=" N ASP I 142 " --> pdb=" O VAL I 138 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL I 144 " --> pdb=" O SER I 140 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL I 145 " --> pdb=" O GLU I 141 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA I 147 " --> pdb=" O SER I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 171 Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 177 through 183 removed outlier: 3.914A pdb=" N ILE I 181 " --> pdb=" O ARG I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 removed outlier: 3.694A pdb=" N PHE I 188 " --> pdb=" O LEU I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 194 Processing helix chain 'I' and resid 197 through 209 removed outlier: 4.089A pdb=" N HIS I 203 " --> pdb=" O PRO I 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 214 Processing helix chain 'I' and resid 215 through 229 Processing helix chain 'I' and resid 232 through 245 Processing helix chain 'I' and resid 266 through 282 removed outlier: 4.001A pdb=" N ALA I 272 " --> pdb=" O LEU I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 378 removed outlier: 3.715A pdb=" N HIS I 374 " --> pdb=" O SER I 370 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N TYR I 375 " --> pdb=" O LEU I 371 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE I 376 " --> pdb=" O LEU I 372 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 402 removed outlier: 4.287A pdb=" N ARG I 387 " --> pdb=" O PRO I 383 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N CYS I 400 " --> pdb=" O LEU I 396 " (cutoff:3.500A) Processing helix chain 'I' and resid 403 through 405 No H-bonds generated for 'chain 'I' and resid 403 through 405' Processing helix chain 'I' and resid 412 through 429 Processing helix chain 'I' and resid 432 through 443 removed outlier: 3.638A pdb=" N ALA I 437 " --> pdb=" O TYR I 433 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS I 441 " --> pdb=" O ALA I 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 459 removed outlier: 3.655A pdb=" N GLN I 457 " --> pdb=" O SER I 453 " (cutoff:3.500A) Processing helix chain 'I' and resid 466 through 471 Processing helix chain 'I' and resid 486 through 514 removed outlier: 3.902A pdb=" N SER I 492 " --> pdb=" O TYR I 488 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP I 511 " --> pdb=" O TRP I 507 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 551 removed outlier: 3.896A pdb=" N MET I 548 " --> pdb=" O SER I 544 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG I 549 " --> pdb=" O THR I 545 " (cutoff:3.500A) Processing helix chain 'I' and resid 554 through 566 removed outlier: 3.663A pdb=" N PHE I 560 " --> pdb=" O PHE I 556 " (cutoff:3.500A) Processing helix chain 'I' and resid 568 through 570 No H-bonds generated for 'chain 'I' and resid 568 through 570' Processing helix chain 'I' and resid 571 through 576 Processing helix chain 'I' and resid 584 through 593 removed outlier: 3.815A pdb=" N SER I 590 " --> pdb=" O GLY I 586 " (cutoff:3.500A) Processing helix chain 'I' and resid 596 through 621 removed outlier: 4.220A pdb=" N GLN I 602 " --> pdb=" O SER I 598 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS I 619 " --> pdb=" O THR I 615 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN I 620 " --> pdb=" O ALA I 616 " (cutoff:3.500A) Processing helix chain 'I' and resid 634 through 651 Processing helix chain 'I' and resid 686 through 695 Processing helix chain 'I' and resid 716 through 726 Processing helix chain 'I' and resid 728 through 736 Processing helix chain 'K' and resid 21 through 46 removed outlier: 3.549A pdb=" N ARG K 26 " --> pdb=" O GLU K 22 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU K 27 " --> pdb=" O GLU K 23 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 77 removed outlier: 4.012A pdb=" N SER K 58 " --> pdb=" O ASN K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 147 removed outlier: 3.778A pdb=" N GLU K 95 " --> pdb=" O THR K 91 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET K 106 " --> pdb=" O GLN K 102 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER K 113 " --> pdb=" O SER K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 183 Processing helix chain 'K' and resid 183 through 188 removed outlier: 3.646A pdb=" N HIS K 187 " --> pdb=" O PHE K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 223 removed outlier: 3.614A pdb=" N ARG K 222 " --> pdb=" O ILE K 218 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 244 Processing helix chain 'L' and resid 27 through 40 Processing helix chain 'L' and resid 60 through 69 removed outlier: 4.430A pdb=" N HIS L 69 " --> pdb=" O ALA L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 105 Processing helix chain 'L' and resid 167 through 172 removed outlier: 3.795A pdb=" N GLU L 172 " --> pdb=" O ASP L 168 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 205 removed outlier: 3.520A pdb=" N ILE L 195 " --> pdb=" O SER L 191 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 226 Processing helix chain 'L' and resid 257 through 269 removed outlier: 3.533A pdb=" N VAL L 268 " --> pdb=" O LEU L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 276 through 296 removed outlier: 3.521A pdb=" N ARG L 293 " --> pdb=" O SER L 289 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS L 294 " --> pdb=" O HIS L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 302 Processing helix chain 'L' and resid 327 through 344 removed outlier: 3.554A pdb=" N PHE L 341 " --> pdb=" O GLU L 337 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 38 removed outlier: 3.825A pdb=" N LEU M 28 " --> pdb=" O GLU M 24 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU M 38 " --> pdb=" O SER M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 83 removed outlier: 3.767A pdb=" N LEU M 78 " --> pdb=" O SER M 74 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR M 81 " --> pdb=" O SER M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 88 removed outlier: 3.704A pdb=" N VAL M 88 " --> pdb=" O LEU M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 124 removed outlier: 3.576A pdb=" N VAL M 117 " --> pdb=" O HIS M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 138 Processing helix chain 'M' and resid 139 through 154 removed outlier: 3.603A pdb=" N GLN M 144 " --> pdb=" O ALA M 140 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG M 145 " --> pdb=" O THR M 141 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE M 152 " --> pdb=" O ARG M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 169 removed outlier: 3.806A pdb=" N LEU M 166 " --> pdb=" O ALA M 162 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER M 167 " --> pdb=" O LEU M 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 14 removed outlier: 3.605A pdb=" N LEU N 14 " --> pdb=" O LYS N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 21 through 28 removed outlier: 3.961A pdb=" N ALA N 27 " --> pdb=" O THR N 23 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TRP N 28 " --> pdb=" O ILE N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 39 removed outlier: 4.101A pdb=" N GLN N 37 " --> pdb=" O GLU N 33 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR N 38 " --> pdb=" O ASN N 34 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL N 39 " --> pdb=" O GLN N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 58 removed outlier: 3.682A pdb=" N VAL N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE N 53 " --> pdb=" O VAL N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 76 removed outlier: 3.751A pdb=" N LEU N 68 " --> pdb=" O SER N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 116 removed outlier: 3.862A pdb=" N ILE N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA N 115 " --> pdb=" O ILE N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 183 removed outlier: 3.529A pdb=" N GLY N 176 " --> pdb=" O THR N 172 " (cutoff:3.500A) Processing helix chain 'N' and resid 197 through 206 removed outlier: 3.713A pdb=" N ALA N 203 " --> pdb=" O ASP N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 241 through 256 removed outlier: 3.504A pdb=" N ARG N 247 " --> pdb=" O VAL N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 301 through 308 removed outlier: 3.571A pdb=" N SER N 308 " --> pdb=" O GLU N 304 " (cutoff:3.500A) Processing helix chain 'N' and resid 320 through 325 Processing helix chain 'O' and resid 96 through 100 Processing helix chain 'O' and resid 101 through 111 removed outlier: 3.614A pdb=" N LEU O 105 " --> pdb=" O VAL O 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 160 through 169 Processing helix chain 'O' and resid 176 through 192 removed outlier: 3.772A pdb=" N GLU O 182 " --> pdb=" O PHE O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 192 through 200 removed outlier: 3.841A pdb=" N ASP O 200 " --> pdb=" O ARG O 196 " (cutoff:3.500A) Processing helix chain 'O' and resid 212 through 215 Processing helix chain 'O' and resid 261 through 278 Processing helix chain 'O' and resid 279 through 282 Processing helix chain 'O' and resid 283 through 291 removed outlier: 3.867A pdb=" N THR O 288 " --> pdb=" O PHE O 284 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG O 289 " --> pdb=" O ALA O 285 " (cutoff:3.500A) Processing helix chain 'O' and resid 292 through 295 removed outlier: 4.052A pdb=" N ASP O 295 " --> pdb=" O GLU O 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 292 through 295' Processing helix chain 'P' and resid 63 through 73 Processing helix chain 'P' and resid 90 through 94 removed outlier: 4.010A pdb=" N MET P 93 " --> pdb=" O SER P 90 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 149 removed outlier: 3.650A pdb=" N CYS P 147 " --> pdb=" O GLU P 143 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU P 149 " --> pdb=" O THR P 145 " (cutoff:3.500A) Processing helix chain 'P' and resid 152 through 157 Processing helix chain 'P' and resid 165 through 191 removed outlier: 4.409A pdb=" N HIS P 171 " --> pdb=" O PHE P 167 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU P 175 " --> pdb=" O HIS P 171 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR P 183 " --> pdb=" O TYR P 179 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU P 189 " --> pdb=" O LYS P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 257 through 269 removed outlier: 4.042A pdb=" N ARG P 263 " --> pdb=" O PRO P 259 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR P 264 " --> pdb=" O LEU P 260 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY P 267 " --> pdb=" O ARG P 263 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU P 269 " --> pdb=" O LEU P 265 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 283 Processing helix chain 'Q' and resid 78 through 99 Processing helix chain 'Q' and resid 103 through 124 removed outlier: 4.126A pdb=" N GLU Q 122 " --> pdb=" O LEU Q 118 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR Q 123 " --> pdb=" O GLN Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 131 through 195 Processing helix chain 'Q' and resid 226 through 231 removed outlier: 3.907A pdb=" N ALA Q 230 " --> pdb=" O LYS Q 226 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU Q 231 " --> pdb=" O GLU Q 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 226 through 231' Processing helix chain 'Q' and resid 236 through 268 removed outlier: 3.538A pdb=" N GLN Q 250 " --> pdb=" O HIS Q 246 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET Q 254 " --> pdb=" O GLN Q 250 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE Q 257 " --> pdb=" O SER Q 253 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 36 removed outlier: 4.046A pdb=" N ARG S 18 " --> pdb=" O SER S 14 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU S 36 " --> pdb=" O GLU S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 72 removed outlier: 3.796A pdb=" N ASN S 60 " --> pdb=" O ARG S 56 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU S 66 " --> pdb=" O ALA S 62 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET S 67 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA S 72 " --> pdb=" O PHE S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 87 Processing helix chain 'S' and resid 89 through 106 removed outlier: 3.819A pdb=" N ASP S 98 " --> pdb=" O LYS S 94 " (cutoff:3.500A) Processing helix chain 'T' and resid 459 through 472 removed outlier: 3.754A pdb=" N PHE T 469 " --> pdb=" O LYS T 465 " (cutoff:3.500A) Processing helix chain 'T' and resid 476 through 505 removed outlier: 3.563A pdb=" N LYS T 485 " --> pdb=" O GLU T 481 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS T 493 " --> pdb=" O LYS T 489 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASP T 496 " --> pdb=" O GLN T 492 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL T 500 " --> pdb=" O ASP T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 511 through 523 removed outlier: 3.561A pdb=" N LEU T 515 " --> pdb=" O LYS T 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU T 518 " --> pdb=" O ASP T 514 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 539 removed outlier: 3.552A pdb=" N LEU T 534 " --> pdb=" O SER T 530 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL T 535 " --> pdb=" O LEU T 531 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU T 536 " --> pdb=" O HIS T 532 " (cutoff:3.500A) Processing helix chain 'T' and resid 540 through 546 removed outlier: 4.360A pdb=" N LEU T 546 " --> pdb=" O GLU T 542 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 30 removed outlier: 3.546A pdb=" N LYS W 23 " --> pdb=" O ARG W 19 " (cutoff:3.500A) Processing helix chain 'W' and resid 38 through 66 Processing helix chain 'W' and resid 71 through 86 removed outlier: 3.648A pdb=" N LYS W 80 " --> pdb=" O LEU W 76 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL W 81 " --> pdb=" O ALA W 77 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS W 84 " --> pdb=" O LYS W 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 23 removed outlier: 3.784A pdb=" N ARG X 17 " --> pdb=" O GLU X 13 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N HIS X 20 " --> pdb=" O SER X 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N HIS X 22 " --> pdb=" O LEU X 18 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE X 23 " --> pdb=" O LEU X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 31 through 60 Processing helix chain 'X' and resid 66 through 81 removed outlier: 3.704A pdb=" N LEU X 70 " --> pdb=" O ASP X 66 " (cutoff:3.500A) Proline residue: X 75 - end of helix removed outlier: 4.282A pdb=" N LEU X 79 " --> pdb=" O PRO X 75 " (cutoff:3.500A) Processing helix chain 'c' and resid 262 through 268 removed outlier: 3.830A pdb=" N LEU c 267 " --> pdb=" O SER c 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 107 removed outlier: 3.845A pdb=" N MET R 101 " --> pdb=" O SER R 97 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU R 102 " --> pdb=" O GLU R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 113 Processing helix chain 'R' and resid 132 through 150 removed outlier: 4.441A pdb=" N MET R 143 " --> pdb=" O THR R 139 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS R 145 " --> pdb=" O GLU R 141 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL R 146 " --> pdb=" O LEU R 142 " (cutoff:3.500A) Processing helix chain 'U' and resid 250 through 268 Proline residue: U 256 - end of helix removed outlier: 3.505A pdb=" N HIS U 262 " --> pdb=" O PHE U 258 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU U 263 " --> pdb=" O GLU U 259 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG U 268 " --> pdb=" O GLU U 264 " (cutoff:3.500A) Processing helix chain 'U' and resid 271 through 366 removed outlier: 4.055A pdb=" N ILE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Proline residue: U 332 - end of helix removed outlier: 3.838A pdb=" N LEU U 351 " --> pdb=" O ARG U 347 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG U 352 " --> pdb=" O LYS U 348 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR U 356 " --> pdb=" O ARG U 352 " (cutoff:3.500A) Processing helix chain 'U' and resid 385 through 403 removed outlier: 3.906A pdb=" N LEU U 398 " --> pdb=" O ALA U 394 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 253 through 254 Processing sheet with id=AA2, first strand: chain 'L' and resid 47 through 48 Processing sheet with id=AA3, first strand: chain 'L' and resid 118 through 123 Processing sheet with id=AA4, first strand: chain 'L' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain 'L' and resid 314 through 315 removed outlier: 5.860A pdb=" N LEU L 304 " --> pdb=" O SER L 242 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N SER L 242 " --> pdb=" O LEU L 304 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ALA L 255 " --> pdb=" O LEU N 294 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE N 297 " --> pdb=" O ALA N 267 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 128 through 130 Processing sheet with id=AA7, first strand: chain 'N' and resid 120 through 122 removed outlier: 3.596A pdb=" N THR N 120 " --> pdb=" O ALA N 136 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA N 136 " --> pdb=" O THR N 120 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA N 130 " --> pdb=" O THR N 126 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR N 126 " --> pdb=" O ALA N 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 120 through 122 removed outlier: 3.596A pdb=" N THR N 120 " --> pdb=" O ALA N 136 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA N 136 " --> pdb=" O THR N 120 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TYR N 151 " --> pdb=" O SER N 164 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR N 155 " --> pdb=" O TYR N 160 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N TYR N 160 " --> pdb=" O TYR N 155 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 114 through 116 removed outlier: 3.994A pdb=" N SER O 114 " --> pdb=" O CYS O 125 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP O 136 " --> pdb=" O THR O 128 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 217 through 221 removed outlier: 3.592A pdb=" N THR O 251 " --> pdb=" O ARG O 236 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 80 through 86 Processing sheet with id=AB3, first strand: chain 'P' and resid 221 through 226 1340 hydrogen bonds defined for protein. 3915 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: 9.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5329 1.33 - 1.45: 4288 1.45 - 1.58: 12826 1.58 - 1.70: 0 1.70 - 1.82: 176 Bond restraints: 22619 Sorted by residual: bond pdb=" N SER Q 99 " pdb=" CA SER Q 99 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.03e+00 bond pdb=" N LEU K 84 " pdb=" CA LEU K 84 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.68e+00 bond pdb=" N PHE O 201 " pdb=" CA PHE O 201 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.24e-02 6.50e+03 7.11e+00 bond pdb=" N TYR P 191 " pdb=" CA TYR P 191 " ideal model delta sigma weight residual 1.457 1.494 -0.038 1.41e-02 5.03e+03 7.10e+00 bond pdb=" N ILE P 141 " pdb=" CA ILE P 141 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.27e-02 6.20e+03 6.50e+00 ... (remaining 22614 not shown) Histogram of bond angle deviations from ideal: 95.99 - 103.60: 205 103.60 - 111.20: 8970 111.20 - 118.81: 9404 118.81 - 126.41: 11743 126.41 - 134.01: 261 Bond angle restraints: 30583 Sorted by residual: angle pdb=" N PHE P 166 " pdb=" CA PHE P 166 " pdb=" C PHE P 166 " ideal model delta sigma weight residual 113.23 104.19 9.04 1.24e+00 6.50e-01 5.32e+01 angle pdb=" N CYS I 156 " pdb=" CA CYS I 156 " pdb=" C CYS I 156 " ideal model delta sigma weight residual 110.80 95.99 14.81 2.13e+00 2.20e-01 4.83e+01 angle pdb=" N VAL P 195 " pdb=" CA VAL P 195 " pdb=" C VAL P 195 " ideal model delta sigma weight residual 107.51 117.59 -10.08 1.49e+00 4.50e-01 4.58e+01 angle pdb=" N ILE I 599 " pdb=" CA ILE I 599 " pdb=" C ILE I 599 " ideal model delta sigma weight residual 112.96 106.40 6.56 1.00e+00 1.00e+00 4.31e+01 angle pdb=" N PRO Q 222 " pdb=" CA PRO Q 222 " pdb=" CB PRO Q 222 " ideal model delta sigma weight residual 103.25 110.03 -6.78 1.05e+00 9.07e-01 4.17e+01 ... (remaining 30578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11710 17.95 - 35.90: 1613 35.90 - 53.85: 373 53.85 - 71.80: 56 71.80 - 89.75: 33 Dihedral angle restraints: 13785 sinusoidal: 5288 harmonic: 8497 Sorted by residual: dihedral pdb=" N ILE Q 100 " pdb=" C ILE Q 100 " pdb=" CA ILE Q 100 " pdb=" CB ILE Q 100 " ideal model delta harmonic sigma weight residual 123.40 105.98 17.42 0 2.50e+00 1.60e-01 4.86e+01 dihedral pdb=" CA TYR N 155 " pdb=" C TYR N 155 " pdb=" N SER N 156 " pdb=" CA SER N 156 " ideal model delta harmonic sigma weight residual -180.00 -151.15 -28.85 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA PHE I 583 " pdb=" C PHE I 583 " pdb=" N PRO I 584 " pdb=" CA PRO I 584 " ideal model delta harmonic sigma weight residual 180.00 152.79 27.21 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 13782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 3478 0.110 - 0.220: 92 0.220 - 0.330: 12 0.330 - 0.440: 0 0.440 - 0.550: 1 Chirality restraints: 3583 Sorted by residual: chirality pdb=" CA ILE Q 100 " pdb=" N ILE Q 100 " pdb=" C ILE Q 100 " pdb=" CB ILE Q 100 " both_signs ideal model delta sigma weight residual False 2.43 2.98 -0.55 2.00e-01 2.50e+01 7.57e+00 chirality pdb=" CA LYS K 233 " pdb=" N LYS K 233 " pdb=" C LYS K 233 " pdb=" CB LYS K 233 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB ILE C 304 " pdb=" CA ILE C 304 " pdb=" CG1 ILE C 304 " pdb=" CG2 ILE C 304 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 3580 not shown) Planarity restraints: 3874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU K 190 " 0.047 5.00e-02 4.00e+02 6.99e-02 7.82e+00 pdb=" N PRO K 191 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO K 191 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO K 191 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO K 240 " -0.043 5.00e-02 4.00e+02 6.52e-02 6.79e+00 pdb=" N PRO K 241 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO K 241 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO K 241 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS P 190 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.86e+00 pdb=" C LYS P 190 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS P 190 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR P 191 " -0.014 2.00e-02 2.50e+03 ... (remaining 3871 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 146 2.47 - 3.08: 15191 3.08 - 3.68: 36720 3.68 - 4.29: 52588 4.29 - 4.90: 83877 Nonbonded interactions: 188522 Sorted by model distance: nonbonded pdb=" O LYS I 155 " pdb=" O CYS I 156 " model vdw 1.860 3.040 nonbonded pdb=" O VAL N 82 " pdb=" OG SER N 165 " model vdw 2.087 2.440 nonbonded pdb=" O TYR O 168 " pdb=" OG1 THR O 171 " model vdw 2.132 2.440 nonbonded pdb=" OH TYR T 543 " pdb=" O ALA W 17 " model vdw 2.133 2.440 nonbonded pdb=" NH1 ARG L 47 " pdb=" OE2 GLU L 337 " model vdw 2.151 2.520 ... (remaining 188517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.440 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: 0.030 Extract box with map and model: 7.700 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 58.070 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.090 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 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 0.051 22619 Z= 0.234 Angle : 0.908 14.807 30583 Z= 0.525 Chirality : 0.048 0.550 3583 Planarity : 0.005 0.079 3874 Dihedral : 17.659 89.751 8199 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.67 % Favored : 93.01 % Rotamer: Outliers : 0.78 % Allowed : 25.04 % Favored : 74.18 % Cbeta Deviations : 0.07 % 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: -2.33 (0.16), residues: 2804 helix: -0.78 (0.12), residues: 1675 sheet: -3.57 (0.30), residues: 213 loop : -2.23 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 150 HIS 0.011 0.001 HIS Q 109 PHE 0.036 0.002 PHE P 120 TYR 0.020 0.002 TYR L 207 ARG 0.011 0.001 ARG I 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 375 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 87 ASN cc_start: 0.7675 (t0) cc_final: 0.7447 (t0) REVERT: H 115 ASN cc_start: 0.8911 (m-40) cc_final: 0.8680 (m110) REVERT: H 187 ASP cc_start: 0.7336 (m-30) cc_final: 0.7132 (m-30) REVERT: I 461 TRP cc_start: 0.8201 (m100) cc_final: 0.7487 (m100) REVERT: K 103 ASP cc_start: 0.6680 (m-30) cc_final: 0.6368 (m-30) REVERT: K 166 MET cc_start: 0.7027 (tpp) cc_final: 0.6390 (tpt) REVERT: P 142 MET cc_start: 0.3716 (mtp) cc_final: 0.3064 (ttt) REVERT: P 165 MET cc_start: 0.6083 (mmt) cc_final: 0.5656 (mmt) REVERT: P 275 LEU cc_start: 0.7208 (mm) cc_final: 0.6964 (pp) REVERT: S 53 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8732 (pp) REVERT: S 85 LEU cc_start: 0.8201 (tp) cc_final: 0.7952 (mt) REVERT: T 493 HIS cc_start: 0.7311 (m-70) cc_final: 0.6854 (m170) REVERT: W 73 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7182 (mm-30) REVERT: X 23 PHE cc_start: 0.4910 (m-10) cc_final: 0.4424 (m-80) REVERT: X 43 LYS cc_start: 0.8576 (ttpt) cc_final: 0.8088 (ttmm) outliers start: 18 outliers final: 3 residues processed: 386 average time/residue: 0.4076 time to fit residues: 236.3653 Evaluate side-chains 316 residues out of total 2630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 312 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain M residue 53 PRO Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain X residue 79 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 237 optimal weight: 10.0000 chunk 212 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 133 optimal weight: 0.1980 chunk 163 optimal weight: 4.9990 chunk 255 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 137 ASN ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 201 ASN I 123 ASN ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 394 GLN I 406 ASN I 554 ASN ** I 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 641 ASN K 39 GLN K 40 ASN K 56 GLN K 73 GLN K 75 GLN ** K 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 GLN ** K 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 269 HIS L 290 HIS ** L 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 ASN M 122 HIS M 125 GLN ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 103 GLN N 106 ASN N 145 ASN N 171 ASN N 186 HIS ** O 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 145 GLN O 185 ASN ** O 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 229 GLN O 281 HIS P 287 ASN Q 83 HIS Q 107 GLN ** Q 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 175 ASN S 10 GLN S 16 GLN ** S 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 105 GLN T 532 HIS ** T 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 71 ASN ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 69 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 22619 Z= 0.339 Angle : 0.739 9.744 30583 Z= 0.379 Chirality : 0.044 0.277 3583 Planarity : 0.005 0.069 3874 Dihedral : 6.341 59.899 3046 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.13 % Favored : 92.58 % Rotamer: Outliers : 4.50 % Allowed : 22.53 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.04 % 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: -2.11 (0.15), residues: 2804 helix: -0.57 (0.12), residues: 1716 sheet: -3.49 (0.32), residues: 192 loop : -2.36 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 150 HIS 0.008 0.001 HIS Q 109 PHE 0.027 0.002 PHE H 96 TYR 0.021 0.002 TYR N 269 ARG 0.007 0.001 ARG O 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 339 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 87 ASN cc_start: 0.7665 (t0) cc_final: 0.7393 (t0) REVERT: H 180 ASN cc_start: 0.8934 (m-40) cc_final: 0.8706 (m-40) REVERT: I 474 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8384 (tt) REVERT: I 596 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7946 (p0) REVERT: I 599 ILE cc_start: 0.8474 (tp) cc_final: 0.8124 (tp) REVERT: I 729 GLN cc_start: 0.7757 (tp40) cc_final: 0.7402 (tp40) REVERT: K 35 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.8025 (mtp) REVERT: K 160 ASN cc_start: 0.9014 (t0) cc_final: 0.8788 (t0) REVERT: K 174 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7614 (tp30) REVERT: K 188 PHE cc_start: 0.7073 (OUTLIER) cc_final: 0.6735 (p90) REVERT: K 215 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7817 (ppp) REVERT: L 207 TYR cc_start: 0.7990 (m-80) cc_final: 0.7540 (m-80) REVERT: L 269 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.7181 (t70) REVERT: M 130 TYR cc_start: 0.8369 (m-80) cc_final: 0.7179 (m-80) REVERT: N 209 TYR cc_start: 0.7826 (p90) cc_final: 0.7591 (p90) REVERT: O 190 ARG cc_start: 0.7382 (tmt170) cc_final: 0.7032 (tmm160) REVERT: O 268 ARG cc_start: 0.6391 (ttp80) cc_final: 0.5314 (tmt-80) REVERT: P 142 MET cc_start: 0.3422 (mtp) cc_final: 0.2968 (ttt) REVERT: P 165 MET cc_start: 0.6103 (mmt) cc_final: 0.5714 (mmt) REVERT: P 275 LEU cc_start: 0.7362 (mm) cc_final: 0.7063 (pp) REVERT: S 52 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8235 (tm-30) REVERT: T 489 LYS cc_start: 0.8396 (tttm) cc_final: 0.8071 (mtpt) REVERT: T 519 MET cc_start: 0.8424 (mmm) cc_final: 0.8216 (mmm) REVERT: X 43 LYS cc_start: 0.8577 (ttpt) cc_final: 0.8056 (ttmm) outliers start: 104 outliers final: 44 residues processed: 415 average time/residue: 0.3433 time to fit residues: 219.0407 Evaluate side-chains 356 residues out of total 2630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 306 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 106 MET Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain I residue 110 ASP Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 234 HIS Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 474 LEU Chi-restraints excluded: chain I residue 544 SER Chi-restraints excluded: chain I residue 596 ASP Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain K residue 188 PHE Chi-restraints excluded: chain K residue 215 MET Chi-restraints excluded: chain K residue 231 TYR Chi-restraints excluded: chain K residue 249 ASN Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 159 THR Chi-restraints excluded: chain L residue 183 LEU Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain L residue 269 HIS Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 53 PRO Chi-restraints excluded: chain N residue 30 PHE Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 291 LEU Chi-restraints excluded: chain O residue 168 TYR Chi-restraints excluded: chain O residue 241 ASP Chi-restraints excluded: chain P residue 279 ILE Chi-restraints excluded: chain Q residue 79 SER Chi-restraints excluded: chain Q residue 164 LYS Chi-restraints excluded: chain S residue 10 GLN Chi-restraints excluded: chain S residue 16 GLN Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 64 ASP Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain W residue 84 LYS Chi-restraints excluded: chain X residue 29 LYS Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain c residue 264 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 141 optimal weight: 6.9990 chunk 79 optimal weight: 0.2980 chunk 212 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 chunk 276 optimal weight: 20.0000 chunk 227 optimal weight: 9.9990 chunk 253 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 205 optimal weight: 20.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 115 ASN ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 638 GLN K 40 ASN K 115 ASN ** K 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 GLN M 125 GLN ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 239 HIS O 100 ASN ** O 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 281 HIS Q 107 GLN ** Q 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 493 HIS ** T 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 22619 Z= 0.533 Angle : 0.816 10.966 30583 Z= 0.416 Chirality : 0.048 0.238 3583 Planarity : 0.005 0.077 3874 Dihedral : 6.567 59.732 3046 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.35 % Favored : 91.44 % Rotamer: Outliers : 5.06 % Allowed : 23.10 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.04 % 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: -2.04 (0.15), residues: 2804 helix: -0.46 (0.12), residues: 1716 sheet: -3.48 (0.33), residues: 188 loop : -2.46 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP P 222 HIS 0.015 0.002 HIS L 269 PHE 0.037 0.003 PHE N 334 TYR 0.042 0.002 TYR Q 108 ARG 0.007 0.001 ARG Q 145 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 312 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 87 ASN cc_start: 0.7710 (t0) cc_final: 0.7445 (t0) REVERT: I 166 ARG cc_start: 0.7654 (mmm160) cc_final: 0.7313 (mmm160) REVERT: I 474 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8386 (tt) REVERT: I 599 ILE cc_start: 0.8641 (tp) cc_final: 0.8335 (tp) REVERT: I 632 PHE cc_start: 0.3940 (OUTLIER) cc_final: 0.3210 (m-80) REVERT: K 21 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7848 (pm20) REVERT: K 166 MET cc_start: 0.7897 (tpt) cc_final: 0.7513 (tpp) REVERT: K 174 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7669 (tp30) REVERT: K 188 PHE cc_start: 0.7192 (OUTLIER) cc_final: 0.6579 (p90) REVERT: K 215 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7444 (tmm) REVERT: L 166 PHE cc_start: 0.8718 (m-80) cc_final: 0.8375 (m-80) REVERT: L 207 TYR cc_start: 0.8125 (m-80) cc_final: 0.7826 (m-80) REVERT: N 209 TYR cc_start: 0.7961 (p90) cc_final: 0.7738 (p90) REVERT: N 266 PHE cc_start: 0.5583 (m-10) cc_final: 0.5279 (m-10) REVERT: P 142 MET cc_start: 0.3798 (mtp) cc_final: 0.3527 (ttt) REVERT: P 165 MET cc_start: 0.5979 (mmt) cc_final: 0.5443 (mmt) REVERT: P 275 LEU cc_start: 0.7680 (mm) cc_final: 0.7169 (pp) REVERT: S 10 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7299 (mp10) REVERT: S 52 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8199 (tm-30) REVERT: X 43 LYS cc_start: 0.8572 (ttpt) cc_final: 0.8069 (ttmm) outliers start: 117 outliers final: 72 residues processed: 397 average time/residue: 0.3358 time to fit residues: 206.7287 Evaluate side-chains 363 residues out of total 2630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 285 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 106 MET Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain I residue 110 ASP Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 234 HIS Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 474 LEU Chi-restraints excluded: chain I residue 601 ASN Chi-restraints excluded: chain I residue 632 PHE Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain I residue 689 LEU Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 115 ASN Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 188 PHE Chi-restraints excluded: chain K residue 215 MET Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 231 TYR Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 249 ASN Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 159 THR Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 183 LEU Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain L residue 329 ILE Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 53 PRO Chi-restraints excluded: chain M residue 131 CYS Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 30 PHE Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 158 THR Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 291 LEU Chi-restraints excluded: chain N residue 326 ILE Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain O residue 168 TYR Chi-restraints excluded: chain O residue 181 CYS Chi-restraints excluded: chain O residue 234 CYS Chi-restraints excluded: chain O residue 241 ASP Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 280 LEU Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain P residue 249 LEU Chi-restraints excluded: chain P residue 279 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 107 GLN Chi-restraints excluded: chain Q residue 164 LYS Chi-restraints excluded: chain S residue 10 GLN Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 64 ASP Chi-restraints excluded: chain T residue 464 VAL Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 84 LYS Chi-restraints excluded: chain X residue 29 LYS Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain c residue 269 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 252 optimal weight: 0.9990 chunk 192 optimal weight: 10.0000 chunk 132 optimal weight: 0.5980 chunk 28 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 171 optimal weight: 0.7980 chunk 256 optimal weight: 3.9990 chunk 271 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 chunk 243 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 ASN ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 ASN ** L 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 125 GLN ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 281 HIS ** Q 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 492 GLN ** T 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 HIS ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22619 Z= 0.254 Angle : 0.692 10.145 30583 Z= 0.353 Chirality : 0.043 0.357 3583 Planarity : 0.005 0.073 3874 Dihedral : 6.279 59.470 3046 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.42 % Favored : 92.37 % Rotamer: Outliers : 4.84 % Allowed : 24.57 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.65 (0.16), residues: 2804 helix: -0.16 (0.12), residues: 1722 sheet: -3.31 (0.33), residues: 185 loop : -2.31 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 150 HIS 0.010 0.001 HIS Q 109 PHE 0.024 0.002 PHE P 120 TYR 0.045 0.002 TYR Q 108 ARG 0.008 0.000 ARG I 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 325 time to evaluate : 2.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 82 ILE cc_start: 0.8607 (mt) cc_final: 0.8400 (mm) REVERT: I 474 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8253 (tt) REVERT: I 632 PHE cc_start: 0.3770 (OUTLIER) cc_final: 0.2945 (m-80) REVERT: I 729 GLN cc_start: 0.7761 (tp40) cc_final: 0.7471 (tp40) REVERT: K 166 MET cc_start: 0.7842 (tpt) cc_final: 0.7442 (tpp) REVERT: K 174 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7682 (tp30) REVERT: K 215 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7550 (tmm) REVERT: L 166 PHE cc_start: 0.8657 (m-80) cc_final: 0.8266 (m-80) REVERT: L 207 TYR cc_start: 0.8012 (m-80) cc_final: 0.7681 (m-80) REVERT: M 130 TYR cc_start: 0.8322 (m-80) cc_final: 0.7259 (m-80) REVERT: O 190 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6598 (tmt170) REVERT: P 275 LEU cc_start: 0.7504 (mm) cc_final: 0.7142 (pp) REVERT: S 56 ARG cc_start: 0.8438 (mtp-110) cc_final: 0.7986 (ptm160) REVERT: T 552 TYR cc_start: 0.6432 (OUTLIER) cc_final: 0.6018 (m-10) REVERT: W 36 GLU cc_start: 0.4886 (OUTLIER) cc_final: 0.3727 (mt-10) REVERT: X 43 LYS cc_start: 0.8527 (ttpt) cc_final: 0.8008 (ttmm) outliers start: 112 outliers final: 61 residues processed: 403 average time/residue: 0.3385 time to fit residues: 209.8654 Evaluate side-chains 365 residues out of total 2630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 298 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 234 HIS Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 426 CYS Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 474 LEU Chi-restraints excluded: chain I residue 632 PHE Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain I residue 689 LEU Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 188 PHE Chi-restraints excluded: chain K residue 215 MET Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 231 TYR Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 249 ASN Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain L residue 329 ILE Chi-restraints excluded: chain L residue 337 GLU Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 30 PHE Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain O residue 168 TYR Chi-restraints excluded: chain O residue 181 CYS Chi-restraints excluded: chain O residue 190 ARG Chi-restraints excluded: chain O residue 241 ASP Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 281 HIS Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain P residue 279 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain S residue 25 TYR Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 64 ASP Chi-restraints excluded: chain T residue 464 VAL Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain W residue 36 GLU Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 84 LYS Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 81 PHE Chi-restraints excluded: chain c residue 269 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 226 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 202 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 231 optimal weight: 8.9990 chunk 187 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 chunk 243 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 236 GLN ** I 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 ASN K 187 HIS ** L 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 269 HIS ** L 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 125 GLN ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 181 ASN Q 184 GLN ** S 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 GLN ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 69 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22619 Z= 0.297 Angle : 0.699 10.038 30583 Z= 0.355 Chirality : 0.044 0.202 3583 Planarity : 0.004 0.081 3874 Dihedral : 6.179 55.419 3043 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.95 % Favored : 91.83 % Rotamer: Outliers : 4.93 % Allowed : 24.74 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.04 % 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: -1.48 (0.16), residues: 2804 helix: -0.01 (0.12), residues: 1727 sheet: -3.20 (0.34), residues: 186 loop : -2.29 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP P 222 HIS 0.022 0.001 HIS O 281 PHE 0.033 0.002 PHE P 120 TYR 0.034 0.002 TYR Q 108 ARG 0.005 0.000 ARG L 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 325 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 205 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: I 474 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8302 (tt) REVERT: I 599 ILE cc_start: 0.8635 (tp) cc_final: 0.8295 (tp) REVERT: I 632 PHE cc_start: 0.3784 (OUTLIER) cc_final: 0.2920 (m-80) REVERT: I 729 GLN cc_start: 0.7761 (tp40) cc_final: 0.7484 (tp40) REVERT: K 45 ILE cc_start: 0.6608 (tp) cc_final: 0.6364 (pt) REVERT: K 166 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7495 (tpp) REVERT: K 215 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7758 (tmm) REVERT: L 166 PHE cc_start: 0.8703 (m-80) cc_final: 0.8337 (m-80) REVERT: L 207 TYR cc_start: 0.8000 (m-80) cc_final: 0.7687 (m-80) REVERT: M 130 TYR cc_start: 0.8337 (m-80) cc_final: 0.7196 (m-80) REVERT: N 21 LEU cc_start: 0.7965 (mm) cc_final: 0.7685 (mm) REVERT: O 190 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6493 (tmt170) REVERT: P 165 MET cc_start: 0.6065 (mmt) cc_final: 0.5669 (mmt) REVERT: P 225 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8322 (tm-30) REVERT: S 10 GLN cc_start: 0.7934 (tt0) cc_final: 0.7354 (mp10) REVERT: S 53 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8682 (tt) REVERT: T 522 GLN cc_start: 0.8072 (mt0) cc_final: 0.7803 (mp10) REVERT: W 36 GLU cc_start: 0.4940 (OUTLIER) cc_final: 0.3814 (mt-10) REVERT: X 43 LYS cc_start: 0.8522 (ttpt) cc_final: 0.8010 (ttmm) outliers start: 114 outliers final: 73 residues processed: 406 average time/residue: 0.3485 time to fit residues: 216.2785 Evaluate side-chains 382 residues out of total 2630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 301 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 106 MET Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 209 THR Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 234 HIS Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 426 CYS Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 474 LEU Chi-restraints excluded: chain I residue 493 VAL Chi-restraints excluded: chain I residue 544 SER Chi-restraints excluded: chain I residue 632 PHE Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain I residue 689 LEU Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 115 ASN Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 188 PHE Chi-restraints excluded: chain K residue 215 MET Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 231 TYR Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 249 ASN Chi-restraints excluded: chain L residue 39 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 183 LEU Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain L residue 329 ILE Chi-restraints excluded: chain L residue 337 GLU Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain N residue 30 PHE Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 167 MET Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain N residue 326 ILE Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain O residue 168 TYR Chi-restraints excluded: chain O residue 181 CYS Chi-restraints excluded: chain O residue 190 ARG Chi-restraints excluded: chain O residue 241 ASP Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 287 PHE Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain P residue 249 LEU Chi-restraints excluded: chain P residue 279 ILE Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain S residue 25 TYR Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 64 ASP Chi-restraints excluded: chain W residue 36 GLU Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 84 LYS Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain c residue 269 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 91 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 159 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 271 optimal weight: 5.9990 chunk 225 optimal weight: 8.9990 chunk 125 optimal weight: 0.5980 chunk 22 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 52 GLN ** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 ASN ** L 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 125 GLN ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 281 HIS Q 120 GLN ** S 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 HIS X 69 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22619 Z= 0.243 Angle : 0.683 9.998 30583 Z= 0.344 Chirality : 0.042 0.231 3583 Planarity : 0.004 0.084 3874 Dihedral : 6.026 57.174 3043 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.38 % Favored : 92.40 % Rotamer: Outliers : 4.97 % Allowed : 25.69 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.29 (0.16), residues: 2804 helix: 0.17 (0.12), residues: 1730 sheet: -3.07 (0.34), residues: 186 loop : -2.29 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP P 222 HIS 0.012 0.001 HIS Q 109 PHE 0.027 0.002 PHE P 120 TYR 0.039 0.002 TYR T 543 ARG 0.005 0.000 ARG O 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 326 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 83 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7785 (mt-10) REVERT: H 96 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.7181 (p90) REVERT: H 205 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: I 474 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8190 (tt) REVERT: I 599 ILE cc_start: 0.8587 (tp) cc_final: 0.8178 (tp) REVERT: I 632 PHE cc_start: 0.4122 (OUTLIER) cc_final: 0.3275 (m-80) REVERT: I 729 GLN cc_start: 0.7658 (tp40) cc_final: 0.7372 (tp40) REVERT: K 21 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7755 (pm20) REVERT: K 166 MET cc_start: 0.7898 (tpt) cc_final: 0.7627 (tpp) REVERT: K 177 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7533 (mt) REVERT: K 215 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7725 (tmm) REVERT: M 130 TYR cc_start: 0.8219 (m-80) cc_final: 0.7048 (m-80) REVERT: N 125 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7002 (tm-30) REVERT: O 190 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7052 (tmm160) REVERT: P 165 MET cc_start: 0.6022 (mmt) cc_final: 0.5598 (mmt) REVERT: P 179 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.5105 (m-80) REVERT: T 552 TYR cc_start: 0.6262 (OUTLIER) cc_final: 0.5850 (m-10) REVERT: X 22 HIS cc_start: 0.5621 (OUTLIER) cc_final: 0.4774 (m170) REVERT: X 43 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8038 (ttmm) outliers start: 115 outliers final: 75 residues processed: 411 average time/residue: 0.3421 time to fit residues: 218.7333 Evaluate side-chains 383 residues out of total 2630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 297 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 52 GLN Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 106 MET Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain I residue 110 ASP Chi-restraints excluded: chain I residue 123 ASN Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 234 HIS Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 426 CYS Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 474 LEU Chi-restraints excluded: chain I residue 544 SER Chi-restraints excluded: chain I residue 632 PHE Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain I residue 689 LEU Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 115 ASN Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 188 PHE Chi-restraints excluded: chain K residue 215 MET Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 231 TYR Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 249 ASN Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 183 LEU Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain L residue 329 ILE Chi-restraints excluded: chain L residue 337 GLU Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 131 CYS Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain N residue 30 PHE Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 167 MET Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain N residue 291 LEU Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 168 TYR Chi-restraints excluded: chain O residue 181 CYS Chi-restraints excluded: chain O residue 190 ARG Chi-restraints excluded: chain O residue 241 ASP Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 281 HIS Chi-restraints excluded: chain O residue 287 PHE Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain S residue 25 TYR Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 64 ASP Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 22 HIS Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain c residue 269 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 262 optimal weight: 30.0000 chunk 30 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 153 optimal weight: 0.4980 chunk 228 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 270 optimal weight: 9.9990 chunk 169 optimal weight: 0.5980 chunk 165 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 125 GLN ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 281 HIS Q 107 GLN ** S 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 HIS X 69 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22619 Z= 0.232 Angle : 0.675 10.444 30583 Z= 0.341 Chirality : 0.042 0.230 3583 Planarity : 0.004 0.085 3874 Dihedral : 5.910 55.755 3043 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.49 % Favored : 92.30 % Rotamer: Outliers : 4.97 % Allowed : 26.90 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.14 (0.16), residues: 2804 helix: 0.29 (0.12), residues: 1735 sheet: -3.02 (0.35), residues: 185 loop : -2.25 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP P 222 HIS 0.017 0.001 HIS O 152 PHE 0.026 0.002 PHE P 120 TYR 0.047 0.002 TYR Q 108 ARG 0.006 0.000 ARG I 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 321 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 83 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7782 (mt-10) REVERT: H 86 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7386 (tm-30) REVERT: H 127 MET cc_start: 0.7487 (mtm) cc_final: 0.7154 (mtm) REVERT: H 204 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7198 (tpt) REVERT: H 205 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7281 (tm-30) REVERT: I 474 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8177 (tt) REVERT: I 599 ILE cc_start: 0.8567 (tp) cc_final: 0.8200 (tp) REVERT: I 632 PHE cc_start: 0.4123 (OUTLIER) cc_final: 0.3116 (m-80) REVERT: I 729 GLN cc_start: 0.7597 (tp40) cc_final: 0.7322 (tp40) REVERT: K 21 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7684 (pm20) REVERT: K 166 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7600 (tpp) REVERT: K 177 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7605 (mt) REVERT: K 215 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7716 (tmm) REVERT: L 166 PHE cc_start: 0.8621 (m-80) cc_final: 0.8335 (m-80) REVERT: M 130 TYR cc_start: 0.8184 (m-80) cc_final: 0.6984 (m-80) REVERT: N 21 LEU cc_start: 0.7845 (mm) cc_final: 0.7555 (mm) REVERT: N 125 GLU cc_start: 0.7436 (tm-30) cc_final: 0.6994 (tm-30) REVERT: O 190 ARG cc_start: 0.7437 (tmt170) cc_final: 0.7042 (tmm160) REVERT: P 89 THR cc_start: 0.4510 (OUTLIER) cc_final: 0.4256 (m) REVERT: P 165 MET cc_start: 0.5974 (mmt) cc_final: 0.5496 (mmt) REVERT: P 179 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.5127 (m-80) REVERT: T 552 TYR cc_start: 0.6288 (OUTLIER) cc_final: 0.5950 (m-10) REVERT: W 73 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7341 (tm-30) outliers start: 115 outliers final: 75 residues processed: 402 average time/residue: 0.3434 time to fit residues: 211.1919 Evaluate side-chains 380 residues out of total 2630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 294 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 106 MET Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain H residue 204 MET Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain I residue 110 ASP Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 234 HIS Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 426 CYS Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 474 LEU Chi-restraints excluded: chain I residue 544 SER Chi-restraints excluded: chain I residue 632 PHE Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain I residue 689 LEU Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 188 PHE Chi-restraints excluded: chain K residue 215 MET Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 249 ASN Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 183 LEU Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain L residue 329 ILE Chi-restraints excluded: chain L residue 337 GLU Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 131 CYS Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain N residue 30 PHE Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 167 MET Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain N residue 291 LEU Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain O residue 100 ASN Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 168 TYR Chi-restraints excluded: chain O residue 169 LEU Chi-restraints excluded: chain O residue 181 CYS Chi-restraints excluded: chain O residue 241 ASP Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 281 HIS Chi-restraints excluded: chain O residue 287 PHE Chi-restraints excluded: chain P residue 89 THR Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 107 GLN Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 64 ASP Chi-restraints excluded: chain T residue 494 LEU Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain c residue 269 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 167 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 161 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 172 optimal weight: 9.9990 chunk 184 optimal weight: 0.3980 chunk 133 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 212 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 52 GLN ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 ASN ** L 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 125 GLN ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 281 HIS P 244 GLN ** S 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22619 Z= 0.246 Angle : 0.703 13.783 30583 Z= 0.350 Chirality : 0.043 0.277 3583 Planarity : 0.004 0.088 3874 Dihedral : 5.868 52.691 3043 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.45 % Favored : 92.37 % Rotamer: Outliers : 4.50 % Allowed : 27.60 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.05 (0.16), residues: 2804 helix: 0.40 (0.12), residues: 1723 sheet: -3.08 (0.36), residues: 173 loop : -2.27 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP P 222 HIS 0.014 0.001 HIS W 44 PHE 0.033 0.002 PHE I 588 TYR 0.036 0.002 TYR Q 108 ARG 0.006 0.000 ARG K 263 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 310 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 83 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7788 (mt-10) REVERT: H 86 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7346 (tm-30) REVERT: H 204 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7257 (tpt) REVERT: H 205 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7294 (tm-30) REVERT: I 168 LEU cc_start: 0.8063 (mt) cc_final: 0.7825 (mt) REVERT: I 474 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8182 (tt) REVERT: I 599 ILE cc_start: 0.8576 (tp) cc_final: 0.8213 (tp) REVERT: I 632 PHE cc_start: 0.4145 (OUTLIER) cc_final: 0.3083 (m-80) REVERT: I 729 GLN cc_start: 0.7549 (tp40) cc_final: 0.7286 (tp40) REVERT: K 177 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7597 (mt) REVERT: L 166 PHE cc_start: 0.8636 (m-80) cc_final: 0.8335 (m-80) REVERT: M 130 TYR cc_start: 0.8189 (m-80) cc_final: 0.6985 (m-80) REVERT: N 21 LEU cc_start: 0.7939 (mm) cc_final: 0.7665 (mm) REVERT: N 125 GLU cc_start: 0.7454 (tm-30) cc_final: 0.6993 (tm-30) REVERT: O 190 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7059 (tmm160) REVERT: P 165 MET cc_start: 0.5841 (mmt) cc_final: 0.5337 (mmt) REVERT: P 179 TYR cc_start: 0.7432 (OUTLIER) cc_final: 0.5196 (m-80) REVERT: P 206 MET cc_start: 0.3220 (tpp) cc_final: 0.2948 (tpp) REVERT: T 543 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.6789 (t80) REVERT: T 552 TYR cc_start: 0.6294 (OUTLIER) cc_final: 0.5947 (m-10) REVERT: W 73 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7340 (tm-30) REVERT: X 22 HIS cc_start: 0.5656 (OUTLIER) cc_final: 0.4780 (m170) outliers start: 104 outliers final: 80 residues processed: 384 average time/residue: 0.3364 time to fit residues: 199.8263 Evaluate side-chains 381 residues out of total 2630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 291 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 GLN Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain H residue 204 MET Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain I residue 110 ASP Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 234 HIS Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 426 CYS Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 474 LEU Chi-restraints excluded: chain I residue 493 VAL Chi-restraints excluded: chain I residue 544 SER Chi-restraints excluded: chain I residue 632 PHE Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain I residue 689 LEU Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 115 ASN Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 188 PHE Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 249 ASN Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 183 LEU Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain L residue 329 ILE Chi-restraints excluded: chain L residue 337 GLU Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 131 CYS Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain N residue 30 PHE Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 167 MET Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain N residue 291 LEU Chi-restraints excluded: chain N residue 323 LEU Chi-restraints excluded: chain N residue 326 ILE Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain O residue 100 ASN Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 168 TYR Chi-restraints excluded: chain O residue 169 LEU Chi-restraints excluded: chain O residue 173 ILE Chi-restraints excluded: chain O residue 181 CYS Chi-restraints excluded: chain O residue 190 ARG Chi-restraints excluded: chain O residue 241 ASP Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 281 HIS Chi-restraints excluded: chain O residue 287 PHE Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain T residue 494 LEU Chi-restraints excluded: chain T residue 543 TYR Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain W residue 41 LEU Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 22 HIS Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain X residue 81 PHE Chi-restraints excluded: chain c residue 269 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 246 optimal weight: 8.9990 chunk 259 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 252 optimal weight: 7.9990 chunk 151 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 chunk 198 optimal weight: 0.9980 chunk 77 optimal weight: 0.2980 chunk 228 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 251 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 52 GLN ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 126 GLN ** L 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 125 GLN ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 281 HIS ** Q 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22619 Z= 0.268 Angle : 0.722 12.703 30583 Z= 0.361 Chirality : 0.044 0.301 3583 Planarity : 0.004 0.092 3874 Dihedral : 5.849 51.664 3043 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.56 % Favored : 92.30 % Rotamer: Outliers : 4.71 % Allowed : 27.60 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.03 (0.16), residues: 2804 helix: 0.41 (0.12), residues: 1725 sheet: -3.14 (0.35), residues: 174 loop : -2.25 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP P 222 HIS 0.014 0.001 HIS Q 109 PHE 0.027 0.002 PHE I 588 TYR 0.047 0.002 TYR Q 108 ARG 0.006 0.000 ARG O 211 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 301 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 83 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7804 (mt-10) REVERT: H 86 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7362 (tm-30) REVERT: H 204 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7321 (tpt) REVERT: H 205 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7314 (tm-30) REVERT: I 168 LEU cc_start: 0.8088 (mt) cc_final: 0.7843 (mt) REVERT: I 474 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8196 (tt) REVERT: I 599 ILE cc_start: 0.8590 (tp) cc_final: 0.8224 (tp) REVERT: I 632 PHE cc_start: 0.4109 (OUTLIER) cc_final: 0.3086 (m-10) REVERT: I 729 GLN cc_start: 0.7558 (tp40) cc_final: 0.7290 (tp40) REVERT: K 21 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: K 177 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7510 (mt) REVERT: K 215 MET cc_start: 0.8564 (ppp) cc_final: 0.8335 (ppp) REVERT: L 166 PHE cc_start: 0.8668 (m-80) cc_final: 0.8311 (m-80) REVERT: M 130 TYR cc_start: 0.8242 (m-80) cc_final: 0.7012 (m-80) REVERT: N 21 LEU cc_start: 0.7958 (mm) cc_final: 0.7678 (mm) REVERT: N 125 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7012 (tm-30) REVERT: O 190 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6680 (tmt170) REVERT: P 89 THR cc_start: 0.4550 (OUTLIER) cc_final: 0.4317 (m) REVERT: P 165 MET cc_start: 0.5975 (mmt) cc_final: 0.5376 (mmt) REVERT: P 179 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.5210 (m-80) REVERT: P 206 MET cc_start: 0.3217 (tpp) cc_final: 0.2985 (tpp) REVERT: S 12 ARG cc_start: 0.7872 (mpp-170) cc_final: 0.7585 (mmm160) REVERT: T 476 GLU cc_start: 0.4106 (mp0) cc_final: 0.3328 (mp0) REVERT: T 552 TYR cc_start: 0.6300 (OUTLIER) cc_final: 0.5951 (m-10) REVERT: W 73 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7363 (tm-30) REVERT: X 22 HIS cc_start: 0.5717 (OUTLIER) cc_final: 0.4817 (m170) outliers start: 109 outliers final: 74 residues processed: 382 average time/residue: 0.3426 time to fit residues: 201.0375 Evaluate side-chains 376 residues out of total 2630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 291 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 GLN Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 106 MET Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 204 MET Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain I residue 110 ASP Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 234 HIS Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 426 CYS Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 474 LEU Chi-restraints excluded: chain I residue 493 VAL Chi-restraints excluded: chain I residue 544 SER Chi-restraints excluded: chain I residue 632 PHE Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain I residue 689 LEU Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 188 PHE Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 249 ASN Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 183 LEU Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain L residue 329 ILE Chi-restraints excluded: chain L residue 337 GLU Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 131 CYS Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain N residue 30 PHE Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 167 MET Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain N residue 291 LEU Chi-restraints excluded: chain N residue 323 LEU Chi-restraints excluded: chain N residue 326 ILE Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain O residue 100 ASN Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 168 TYR Chi-restraints excluded: chain O residue 169 LEU Chi-restraints excluded: chain O residue 173 ILE Chi-restraints excluded: chain O residue 181 CYS Chi-restraints excluded: chain O residue 190 ARG Chi-restraints excluded: chain O residue 241 ASP Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 281 HIS Chi-restraints excluded: chain O residue 287 PHE Chi-restraints excluded: chain P residue 89 THR Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 64 ASP Chi-restraints excluded: chain T residue 494 LEU Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain W residue 41 LEU Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 22 HIS Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain c residue 269 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 165 optimal weight: 0.9990 chunk 266 optimal weight: 5.9990 chunk 162 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 chunk 185 optimal weight: 4.9990 chunk 279 optimal weight: 7.9990 chunk 257 optimal weight: 8.9990 chunk 222 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 52 GLN ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 HIS ** I 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 125 GLN ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 281 HIS ** Q 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 22619 Z= 0.381 Angle : 0.791 13.186 30583 Z= 0.394 Chirality : 0.046 0.374 3583 Planarity : 0.005 0.097 3874 Dihedral : 6.020 51.678 3043 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.35 % Favored : 91.51 % Rotamer: Outliers : 4.02 % Allowed : 28.20 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.04 % 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: -1.12 (0.16), residues: 2804 helix: 0.34 (0.13), residues: 1713 sheet: -3.10 (0.34), residues: 180 loop : -2.26 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP P 222 HIS 0.016 0.002 HIS W 44 PHE 0.032 0.002 PHE M 92 TYR 0.052 0.002 TYR Q 108 ARG 0.006 0.001 ARG L 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 304 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 MET cc_start: 0.6830 (tpp) cc_final: 0.6625 (mmt) REVERT: H 83 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7842 (mt-10) REVERT: H 96 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7294 (p90) REVERT: H 204 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7289 (tpt) REVERT: I 168 LEU cc_start: 0.8110 (mt) cc_final: 0.7883 (mt) REVERT: I 474 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8280 (tt) REVERT: I 599 ILE cc_start: 0.8630 (tp) cc_final: 0.8313 (tp) REVERT: I 632 PHE cc_start: 0.4037 (OUTLIER) cc_final: 0.2995 (m-80) REVERT: I 729 GLN cc_start: 0.7660 (tp40) cc_final: 0.7357 (tp40) REVERT: K 174 GLU cc_start: 0.7929 (tp30) cc_final: 0.7703 (tp30) REVERT: K 177 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7663 (mt) REVERT: K 215 MET cc_start: 0.8591 (ppp) cc_final: 0.8361 (ppp) REVERT: L 166 PHE cc_start: 0.8753 (m-80) cc_final: 0.8371 (m-80) REVERT: M 130 TYR cc_start: 0.8392 (m-80) cc_final: 0.7311 (m-80) REVERT: N 21 LEU cc_start: 0.8216 (mm) cc_final: 0.7834 (mm) REVERT: N 125 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7064 (tm-30) REVERT: O 190 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7060 (tmt170) REVERT: P 179 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.5229 (m-80) REVERT: S 12 ARG cc_start: 0.7857 (mpp-170) cc_final: 0.7529 (mmm160) REVERT: T 476 GLU cc_start: 0.4219 (mp0) cc_final: 0.3465 (mp0) REVERT: T 552 TYR cc_start: 0.6149 (OUTLIER) cc_final: 0.5798 (m-10) REVERT: W 73 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7331 (tm-30) REVERT: X 22 HIS cc_start: 0.5900 (OUTLIER) cc_final: 0.5017 (m170) REVERT: X 74 LEU cc_start: 0.6710 (mt) cc_final: 0.6447 (mt) outliers start: 93 outliers final: 73 residues processed: 373 average time/residue: 0.3491 time to fit residues: 199.2845 Evaluate side-chains 375 residues out of total 2630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 293 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 52 GLN Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 204 MET Chi-restraints excluded: chain I residue 110 ASP Chi-restraints excluded: chain I residue 150 TRP Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 234 HIS Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 426 CYS Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain I residue 443 LEU Chi-restraints excluded: chain I residue 474 LEU Chi-restraints excluded: chain I residue 493 VAL Chi-restraints excluded: chain I residue 544 SER Chi-restraints excluded: chain I residue 632 PHE Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain I residue 689 LEU Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 188 PHE Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 249 ASN Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 183 LEU Chi-restraints excluded: chain L residue 230 MET Chi-restraints excluded: chain L residue 300 SER Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain L residue 329 ILE Chi-restraints excluded: chain L residue 337 GLU Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 131 CYS Chi-restraints excluded: chain M residue 134 GLU Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain N residue 30 PHE Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 156 SER Chi-restraints excluded: chain N residue 167 MET Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain N residue 291 LEU Chi-restraints excluded: chain N residue 323 LEU Chi-restraints excluded: chain N residue 326 ILE Chi-restraints excluded: chain N residue 331 MET Chi-restraints excluded: chain O residue 100 ASN Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 168 TYR Chi-restraints excluded: chain O residue 173 ILE Chi-restraints excluded: chain O residue 181 CYS Chi-restraints excluded: chain O residue 190 ARG Chi-restraints excluded: chain O residue 241 ASP Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 281 HIS Chi-restraints excluded: chain O residue 287 PHE Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 219 VAL Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 64 ASP Chi-restraints excluded: chain T residue 494 LEU Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 22 HIS Chi-restraints excluded: chain X residue 79 LEU Chi-restraints excluded: chain c residue 269 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 177 optimal weight: 0.8980 chunk 237 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 205 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 223 optimal weight: 4.9990 chunk 93 optimal weight: 0.2980 chunk 229 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 0.0270 overall best weight: 0.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 52 GLN ** H 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 201 ASN ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.169212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.122028 restraints weight = 38594.047| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.85 r_work: 0.3593 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22619 Z= 0.235 Angle : 0.739 12.475 30583 Z= 0.366 Chirality : 0.044 0.306 3583 Planarity : 0.004 0.093 3874 Dihedral : 5.851 50.740 3043 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.52 % Favored : 92.37 % Rotamer: Outliers : 3.81 % Allowed : 28.89 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.94 (0.16), residues: 2804 helix: 0.46 (0.13), residues: 1706 sheet: -3.39 (0.37), residues: 149 loop : -2.11 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP P 222 HIS 0.015 0.001 HIS Q 109 PHE 0.032 0.002 PHE M 92 TYR 0.052 0.002 TYR Q 108 ARG 0.013 0.001 ARG P 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5610.61 seconds wall clock time: 102 minutes 30.79 seconds (6150.79 seconds total)