Starting phenix.real_space_refine on Fri Apr 12 07:06:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8o_21107/04_2024/6v8o_21107.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8o_21107/04_2024/6v8o_21107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8o_21107/04_2024/6v8o_21107.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8o_21107/04_2024/6v8o_21107.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8o_21107/04_2024/6v8o_21107.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8o_21107/04_2024/6v8o_21107.pdb" } resolution = 3.07 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= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 91 5.16 5 C 15930 2.51 5 N 4277 2.21 5 O 4804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 278": "NH1" <-> "NH2" Residue "I PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 143": "NH1" <-> "NH2" Residue "L PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 225": "NH1" <-> "NH2" Residue "M TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 198": "NH1" <-> "NH2" Residue "O ARG 217": "NH1" <-> "NH2" Residue "O ASP 256": "OD1" <-> "OD2" Residue "O TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 244": "OE1" <-> "OE2" Residue "R TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 308": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 25103 Number of models: 1 Model: "" Number of chains: 23 Chain: "C" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 493 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "D" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 772 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain breaks: 1 Chain: "E" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 978 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "F" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 536 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 7, 'TRANS': 59} Chain breaks: 1 Chain: "G" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 422 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "H" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1083 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain breaks: 1 Chain: "I" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2416 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Chain: "J" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'TRANS': 114} Chain: "K" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 878 Classifications: {'peptide': 109} Link IDs: {'TRANS': 108} Chain breaks: 1 Chain: "L" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2445 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 2 Chain: "M" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2474 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 16, 'TRANS': 293} Chain breaks: 3 Chain: "N" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3275 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 18, 'TRANS': 393} Chain breaks: 1 Chain: "O" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3145 Classifications: {'peptide': 384} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 361} Chain breaks: 3 Chain: "Q" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2137 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 12, 'TRANS': 251} Chain breaks: 2 Chain: "R" Number of atoms: 2126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2126 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 11, 'TRANS': 250} Chain breaks: 1 Chain: "S" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 278 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "2" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 140 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'UNK:plan-1': 28} Unresolved non-hydrogen planarities: 28 Chain: "3" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "4" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "5" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "6" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "7" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 245 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'UNK:plan-1': 49} Unresolved non-hydrogen planarities: 49 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5813 SG CYS I 260 150.361 54.662 77.002 1.00 50.60 S ATOM 5836 SG CYS I 263 153.627 52.802 78.258 1.00 55.54 S ATOM 5999 SG CYS I 283 152.020 55.587 80.436 1.00 54.74 S ATOM 6022 SG CYS I 286 153.971 56.119 76.846 1.00 50.21 S Time building chain proxies: 13.12, per 1000 atoms: 0.52 Number of scatterers: 25103 At special positions: 0 Unit cell: (208.655, 130.949, 198.582, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 91 16.00 O 4804 8.00 N 4277 7.00 C 15930 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: 9.89 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 601 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 260 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 263 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 286 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 283 " Number of angles added : 6 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6118 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 17 sheets defined 56.4% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'C' and resid 20 through 40 Processing helix chain 'C' and resid 45 through 54 Processing helix chain 'C' and resid 54 through 75 Processing helix chain 'D' and resid 7 through 18 Processing helix chain 'D' and resid 27 through 35 Processing helix chain 'D' and resid 72 through 79 Processing helix chain 'D' and resid 93 through 99 Processing helix chain 'D' and resid 101 through 113 removed outlier: 3.601A pdb=" N PHE D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 125 Processing helix chain 'E' and resid 318 through 343 Processing helix chain 'E' and resid 400 through 404 removed outlier: 4.236A pdb=" N SER E 403 " --> pdb=" O THR E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 411 removed outlier: 4.272A pdb=" N TYR E 410 " --> pdb=" O PRO E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 433 Processing helix chain 'F' and resid 862 through 867 Processing helix chain 'F' and resid 871 through 881 removed outlier: 3.765A pdb=" N MET F 881 " --> pdb=" O HIS F 877 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 196 removed outlier: 3.906A pdb=" N ILE G 177 " --> pdb=" O THR G 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 468 Processing helix chain 'I' and resid 58 through 72 Processing helix chain 'I' and resid 95 through 102 Processing helix chain 'I' and resid 103 through 106 Processing helix chain 'I' and resid 114 through 132 removed outlier: 3.756A pdb=" N SER I 132 " --> pdb=" O THR I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 146 removed outlier: 3.845A pdb=" N VAL I 142 " --> pdb=" O THR I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 163 removed outlier: 3.512A pdb=" N TRP I 163 " --> pdb=" O PHE I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 175 removed outlier: 4.099A pdb=" N LYS I 175 " --> pdb=" O PRO I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 244 Processing helix chain 'I' and resid 246 through 251 Processing helix chain 'I' and resid 283 through 289 Processing helix chain 'I' and resid 297 through 299 No H-bonds generated for 'chain 'I' and resid 297 through 299' Processing helix chain 'I' and resid 316 through 330 Processing helix chain 'I' and resid 333 through 342 removed outlier: 3.847A pdb=" N GLY I 342 " --> pdb=" O ALA I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 356 Processing helix chain 'I' and resid 360 through 368 Processing helix chain 'J' and resid 388 through 403 removed outlier: 3.624A pdb=" N CYS J 392 " --> pdb=" O LYS J 388 " (cutoff:3.500A) Processing helix chain 'J' and resid 406 through 490 removed outlier: 3.834A pdb=" N VAL J 410 " --> pdb=" O LYS J 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 388 through 402 Processing helix chain 'K' and resid 421 through 489 Processing helix chain 'L' and resid 59 through 76 Processing helix chain 'L' and resid 83 through 87 Processing helix chain 'L' and resid 96 through 102 Processing helix chain 'L' and resid 114 through 131 Processing helix chain 'L' and resid 138 through 145 removed outlier: 4.076A pdb=" N VAL L 142 " --> pdb=" O THR L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 163 Processing helix chain 'L' and resid 171 through 175 removed outlier: 3.541A pdb=" N LYS L 175 " --> pdb=" O PRO L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 292 Processing helix chain 'L' and resid 298 through 304 Processing helix chain 'L' and resid 316 through 330 Processing helix chain 'L' and resid 333 through 342 Processing helix chain 'L' and resid 346 through 356 Processing helix chain 'L' and resid 360 through 377 removed outlier: 3.583A pdb=" N ILE L 364 " --> pdb=" O GLU L 360 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 51 Processing helix chain 'M' and resid 237 through 242 removed outlier: 3.629A pdb=" N LEU M 241 " --> pdb=" O ASN M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 263 Processing helix chain 'M' and resid 268 through 275 Processing helix chain 'M' and resid 316 through 324 Processing helix chain 'M' and resid 331 through 342 removed outlier: 3.623A pdb=" N VAL M 335 " --> pdb=" O PRO M 331 " (cutoff:3.500A) Processing helix chain 'M' and resid 372 through 377 Processing helix chain 'M' and resid 387 through 425 Processing helix chain 'M' and resid 425 through 445 Processing helix chain 'M' and resid 452 through 457 Processing helix chain 'M' and resid 470 through 472 No H-bonds generated for 'chain 'M' and resid 470 through 472' Processing helix chain 'M' and resid 473 through 480 Processing helix chain 'N' and resid 40 through 46 Processing helix chain 'N' and resid 65 through 70 removed outlier: 3.923A pdb=" N SER N 70 " --> pdb=" O VAL N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 92 removed outlier: 3.995A pdb=" N GLY N 92 " --> pdb=" O ALA N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 111 Processing helix chain 'N' and resid 123 through 140 removed outlier: 3.664A pdb=" N PHE N 127 " --> pdb=" O LEU N 123 " (cutoff:3.500A) Proline residue: N 133 - end of helix Processing helix chain 'N' and resid 148 through 170 Processing helix chain 'N' and resid 171 through 180 removed outlier: 3.691A pdb=" N LYS N 180 " --> pdb=" O GLN N 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 201 Processing helix chain 'N' and resid 208 through 210 No H-bonds generated for 'chain 'N' and resid 208 through 210' Processing helix chain 'N' and resid 211 through 231 removed outlier: 3.878A pdb=" N SER N 231 " --> pdb=" O GLU N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 240 through 253 Processing helix chain 'N' and resid 255 through 269 removed outlier: 3.614A pdb=" N VAL N 259 " --> pdb=" O ASP N 255 " (cutoff:3.500A) Processing helix chain 'N' and resid 279 through 284 removed outlier: 3.521A pdb=" N ASP N 282 " --> pdb=" O SER N 279 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU N 284 " --> pdb=" O ALA N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 285 through 298 removed outlier: 3.565A pdb=" N LEU N 298 " --> pdb=" O SER N 294 " (cutoff:3.500A) Processing helix chain 'N' and resid 301 through 317 Processing helix chain 'N' and resid 320 through 329 removed outlier: 4.334A pdb=" N SER N 329 " --> pdb=" O GLU N 325 " (cutoff:3.500A) Processing helix chain 'N' and resid 329 through 345 Proline residue: N 341 - end of helix removed outlier: 3.681A pdb=" N SER N 345 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'N' and resid 353 through 359 removed outlier: 3.800A pdb=" N GLN N 357 " --> pdb=" O TYR N 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 524 through 539 removed outlier: 3.651A pdb=" N ASN N 539 " --> pdb=" O CYS N 535 " (cutoff:3.500A) Processing helix chain 'N' and resid 546 through 564 removed outlier: 3.749A pdb=" N CYS N 550 " --> pdb=" O GLY N 546 " (cutoff:3.500A) Proline residue: N 555 - end of helix Processing helix chain 'N' and resid 564 through 571 removed outlier: 3.513A pdb=" N THR N 568 " --> pdb=" O ILE N 564 " (cutoff:3.500A) Processing helix chain 'N' and resid 571 through 577 Processing helix chain 'O' and resid 10 through 25 Processing helix chain 'O' and resid 29 through 33 Processing helix chain 'O' and resid 43 through 45 No H-bonds generated for 'chain 'O' and resid 43 through 45' Processing helix chain 'O' and resid 46 through 61 Processing helix chain 'O' and resid 75 through 82 removed outlier: 3.518A pdb=" N ARG O 79 " --> pdb=" O THR O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 110 removed outlier: 3.500A pdb=" N PHE O 92 " --> pdb=" O ILE O 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 114 through 138 removed outlier: 3.532A pdb=" N GLN O 118 " --> pdb=" O THR O 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 170 through 179 Processing helix chain 'O' and resid 243 through 248 removed outlier: 4.029A pdb=" N VAL O 247 " --> pdb=" O ARG O 243 " (cutoff:3.500A) Processing helix chain 'O' and resid 302 through 314 Processing helix chain 'O' and resid 389 through 394 Processing helix chain 'O' and resid 403 through 412 removed outlier: 3.659A pdb=" N ILE O 407 " --> pdb=" O GLY O 403 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 436 removed outlier: 3.656A pdb=" N ASN O 436 " --> pdb=" O GLU O 432 " (cutoff:3.500A) Processing helix chain 'O' and resid 442 through 462 Processing helix chain 'Q' and resid 3 through 7 Processing helix chain 'Q' and resid 15 through 22 Processing helix chain 'Q' and resid 161 through 167 Processing helix chain 'Q' and resid 168 through 177 Processing helix chain 'Q' and resid 231 through 244 Processing helix chain 'Q' and resid 247 through 265 removed outlier: 3.553A pdb=" N LEU Q 265 " --> pdb=" O GLN Q 261 " (cutoff:3.500A) Processing helix chain 'Q' and resid 265 through 270 removed outlier: 3.629A pdb=" N ALA Q 270 " --> pdb=" O GLU Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 319 Processing helix chain 'Q' and resid 323 through 345 removed outlier: 4.018A pdb=" N LEU Q 327 " --> pdb=" O GLU Q 323 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER Q 329 " --> pdb=" O ILE Q 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 66 Processing helix chain 'R' and resid 68 through 73 Processing helix chain 'R' and resid 74 through 102 removed outlier: 3.502A pdb=" N ALA R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 127 Processing helix chain 'R' and resid 132 through 136 removed outlier: 4.081A pdb=" N LEU R 136 " --> pdb=" O ASP R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 172 removed outlier: 3.548A pdb=" N LEU R 172 " --> pdb=" O LYS R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 179 removed outlier: 4.106A pdb=" N PHE R 178 " --> pdb=" O GLU R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 208 Processing helix chain 'R' and resid 236 through 250 Processing helix chain 'R' and resid 250 through 267 Processing helix chain 'R' and resid 268 through 273 Processing helix chain 'R' and resid 273 through 278 Processing helix chain 'R' and resid 279 through 290 removed outlier: 3.635A pdb=" N GLN R 290 " --> pdb=" O GLN R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 318 Processing helix chain 'S' and resid 204 through 227 removed outlier: 3.744A pdb=" N GLN S 227 " --> pdb=" O LEU S 223 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 20 Processing helix chain '4' and resid 1 through 18 Processing helix chain '5' and resid 4 through 16 Processing helix chain '6' and resid 421 through 434 Processing sheet with id=AA1, first strand: chain 'E' and resid 349 through 351 removed outlier: 3.734A pdb=" N GLY L 180 " --> pdb=" O ILE E 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 368 through 373 removed outlier: 6.977A pdb=" N VAL E 368 " --> pdb=" O ASP I 192 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASP I 192 " --> pdb=" O VAL E 368 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY E 370 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL E 385 " --> pdb=" O PHE I 187 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL I 189 " --> pdb=" O VAL E 385 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU E 387 " --> pdb=" O VAL I 189 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU I 191 " --> pdb=" O GLU E 387 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL E 389 " --> pdb=" O LEU I 191 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS I 231 " --> pdb=" O THR E 388 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE E 390 " --> pdb=" O THR I 229 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N THR I 229 " --> pdb=" O ILE E 390 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 157 through 160 removed outlier: 3.503A pdb=" N SER S 201 " --> pdb=" O ASN G 157 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 589 through 594 removed outlier: 4.072A pdb=" N HIS H 514 " --> pdb=" O GLN H 453 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLN H 453 " --> pdb=" O HIS H 514 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER H 458 " --> pdb=" O VAL H 482 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL H 482 " --> pdb=" O SER H 458 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP H 481 " --> pdb=" O ILE L 259 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N HIS L 261 " --> pdb=" O TRP H 481 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU H 483 " --> pdb=" O HIS L 261 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR L 262 " --> pdb=" O ASN L 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 522 through 526 removed outlier: 6.052A pdb=" N PHE H 498 " --> pdb=" O TRP H 620 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ASN H 622 " --> pdb=" O PHE H 498 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE H 500 " --> pdb=" O ASN H 622 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA H 497 " --> pdb=" O ILE O 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 80 through 83 Processing sheet with id=AA7, first strand: chain 'I' and resid 256 through 257 removed outlier: 3.664A pdb=" N VAL N 47 " --> pdb=" O VAL I 257 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 281 through 282 Processing sheet with id=AA9, first strand: chain 'K' and resid 493 through 497 Processing sheet with id=AB1, first strand: chain 'M' and resid 368 through 369 removed outlier: 3.543A pdb=" N LEU M 368 " --> pdb=" O ILE M 76 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG M 75 " --> pdb=" O UNK 7 24 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR M 77 " --> pdb=" O UNK 7 26 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR M 79 " --> pdb=" O UNK 7 28 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 349 through 352 removed outlier: 6.582A pdb=" N SER M 219 " --> pdb=" O UNK 7 62 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N UNK 7 64 " --> pdb=" O SER M 219 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR M 221 " --> pdb=" O UNK 7 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 246 through 247 Processing sheet with id=AB4, first strand: chain 'M' and resid 313 through 314 removed outlier: 3.531A pdb=" N LEU M 330 " --> pdb=" O VAL M 313 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 476 through 477 Processing sheet with id=AB6, first strand: chain 'Q' and resid 13 through 14 removed outlier: 3.566A pdb=" N LYS Q 179 " --> pdb=" O SER Q 14 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 203 through 212 Processing sheet with id=AB8, first strand: chain 'Q' and resid 278 through 286 1297 hydrogen bonds defined for protein. 3765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.28 Time building geometry restraints manager: 10.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8274 1.34 - 1.46: 4234 1.46 - 1.57: 12890 1.57 - 1.69: 0 1.69 - 1.81: 145 Bond restraints: 25543 Sorted by residual: bond pdb=" CB TRP I 163 " pdb=" CG TRP I 163 " ideal model delta sigma weight residual 1.498 1.463 0.035 3.10e-02 1.04e+03 1.30e+00 bond pdb=" CA LEU N 132 " pdb=" C LEU N 132 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.26e-02 6.30e+03 1.20e+00 bond pdb=" C TYR O 85 " pdb=" N GLU O 86 " ideal model delta sigma weight residual 1.329 1.297 0.031 3.03e-02 1.09e+03 1.08e+00 bond pdb=" C LEU N 132 " pdb=" O LEU N 132 " ideal model delta sigma weight residual 1.238 1.251 -0.013 1.28e-02 6.10e+03 1.07e+00 bond pdb=" C PHE R 135 " pdb=" N LEU R 136 " ideal model delta sigma weight residual 1.332 1.318 0.014 1.40e-02 5.10e+03 9.94e-01 ... (remaining 25538 not shown) Histogram of bond angle deviations from ideal: 99.87 - 106.91: 679 106.91 - 113.96: 15088 113.96 - 121.00: 12092 121.00 - 128.05: 6521 128.05 - 135.09: 175 Bond angle restraints: 34555 Sorted by residual: angle pdb=" N SER Q 374 " pdb=" CA SER Q 374 " pdb=" C SER Q 374 " ideal model delta sigma weight residual 110.80 120.59 -9.79 2.13e+00 2.20e-01 2.11e+01 angle pdb=" C ILE H 528 " pdb=" N ASN H 529 " pdb=" CA ASN H 529 " ideal model delta sigma weight residual 121.54 129.75 -8.21 1.91e+00 2.74e-01 1.85e+01 angle pdb=" C GLY Q 373 " pdb=" N SER Q 374 " pdb=" CA SER Q 374 " ideal model delta sigma weight residual 121.54 129.11 -7.57 1.91e+00 2.74e-01 1.57e+01 angle pdb=" N PRO O 415 " pdb=" CA PRO O 415 " pdb=" C PRO O 415 " ideal model delta sigma weight residual 114.18 110.44 3.74 1.39e+00 5.18e-01 7.23e+00 angle pdb=" C SER Q 374 " pdb=" CA SER Q 374 " pdb=" CB SER Q 374 " ideal model delta sigma weight residual 110.42 105.22 5.20 1.99e+00 2.53e-01 6.84e+00 ... (remaining 34550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 14796 17.77 - 35.54: 707 35.54 - 53.31: 140 53.31 - 71.09: 34 71.09 - 88.86: 6 Dihedral angle restraints: 15683 sinusoidal: 6343 harmonic: 9340 Sorted by residual: dihedral pdb=" CA GLU Q 371 " pdb=" C GLU Q 371 " pdb=" N LEU Q 372 " pdb=" CA LEU Q 372 " ideal model delta harmonic sigma weight residual -180.00 -153.93 -26.07 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ASN H 529 " pdb=" C ASN H 529 " pdb=" N LYS H 530 " pdb=" CA LYS H 530 " ideal model delta harmonic sigma weight residual 180.00 155.34 24.66 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLY Q 373 " pdb=" C GLY Q 373 " pdb=" N SER Q 374 " pdb=" CA SER Q 374 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 15680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2642 0.033 - 0.066: 973 0.066 - 0.099: 233 0.099 - 0.133: 118 0.133 - 0.166: 5 Chirality restraints: 3971 Sorted by residual: chirality pdb=" CA ILE E 359 " pdb=" N ILE E 359 " pdb=" C ILE E 359 " pdb=" CB ILE E 359 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA ILE N 514 " pdb=" N ILE N 514 " pdb=" C ILE N 514 " pdb=" CB ILE N 514 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA SER Q 374 " pdb=" N SER Q 374 " pdb=" C SER Q 374 " pdb=" CB SER Q 374 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 3968 not shown) Planarity restraints: 4440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE N 564 " -0.048 5.00e-02 4.00e+02 7.37e-02 8.70e+00 pdb=" N PRO N 565 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO N 565 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO N 565 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN M 6 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO M 7 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO M 7 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO M 7 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU N 124 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO N 125 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO N 125 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO N 125 " -0.025 5.00e-02 4.00e+02 ... (remaining 4437 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 668 2.70 - 3.25: 25129 3.25 - 3.80: 37366 3.80 - 4.35: 48918 4.35 - 4.90: 82429 Nonbonded interactions: 194510 Sorted by model distance: nonbonded pdb=" O GLU N 227 " pdb=" OG SER N 230 " model vdw 2.149 2.440 nonbonded pdb=" OH TYR Q 184 " pdb=" OD1 ASP Q 242 " model vdw 2.150 2.440 nonbonded pdb=" OE2 GLU O 41 " pdb=" OG SER O 50 " model vdw 2.163 2.440 nonbonded pdb=" O LYS H 449 " pdb=" OG1 THR H 516 " model vdw 2.164 2.440 nonbonded pdb=" OD1 ASN Q 282 " pdb=" ND2 ASN Q 295 " model vdw 2.201 2.520 ... (remaining 194505 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '3' selection = chain '4' } ncs_group { reference = chain '5' selection = (chain '6' and resid 421 through 434) } ncs_group { reference = (chain 'I' and (resid 58 through 304 or resid 312 through 368)) selection = (chain 'L' and (resid 58 through 202 or resid 222 through 368)) } ncs_group { reference = (chain 'J' and (resid 387 through 402 or resid 420 through 501)) selection = (chain 'K' and resid 387 through 501) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.890 Check model and map are aligned: 0.400 Set scattering table: 0.270 Process input model: 68.910 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.160 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 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 0.050 25543 Z= 0.272 Angle : 0.549 14.790 34555 Z= 0.299 Chirality : 0.039 0.166 3971 Planarity : 0.003 0.074 4440 Dihedral : 11.206 88.857 9565 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.89 % Favored : 93.01 % Rotamer: Outliers : 2.31 % Allowed : 5.62 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -1.57 (0.14), residues: 2946 helix: 0.34 (0.13), residues: 1511 sheet: -0.89 (0.36), residues: 187 loop : -2.91 (0.15), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP O 273 HIS 0.004 0.001 HIS N 220 PHE 0.012 0.001 PHE I 85 TYR 0.015 0.001 TYR I 272 ARG 0.003 0.000 ARG Q 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 682 time to evaluate : 3.019 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: C 48 ARG cc_start: 0.7326 (ttt90) cc_final: 0.7065 (tmt170) REVERT: D 94 ARG cc_start: 0.6705 (ttt180) cc_final: 0.6372 (ttt-90) REVERT: D 107 HIS cc_start: 0.7234 (t70) cc_final: 0.6968 (t-90) REVERT: E 329 ARG cc_start: 0.7079 (mtm110) cc_final: 0.6539 (mmt180) REVERT: E 353 TYR cc_start: 0.8604 (m-80) cc_final: 0.8031 (m-80) REVERT: E 430 LYS cc_start: 0.8227 (mttt) cc_final: 0.8021 (mtmt) REVERT: F 817 ARG cc_start: 0.6858 (mtp180) cc_final: 0.6477 (mtp85) REVERT: G 167 MET cc_start: 0.8383 (ttm) cc_final: 0.7454 (mtp) REVERT: G 189 LEU cc_start: 0.7023 (mt) cc_final: 0.6772 (mt) REVERT: I 191 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7780 (pp) REVERT: I 255 HIS cc_start: 0.6476 (p-80) cc_final: 0.6193 (m170) REVERT: I 281 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8570 (m-40) REVERT: J 388 LYS cc_start: 0.7808 (mttt) cc_final: 0.7329 (mppt) REVERT: J 390 MET cc_start: 0.7978 (mmm) cc_final: 0.7726 (mmm) REVERT: J 394 ASN cc_start: 0.8741 (m-40) cc_final: 0.8443 (m110) REVERT: J 437 MET cc_start: 0.7769 (mmm) cc_final: 0.7245 (mmt) REVERT: K 475 LEU cc_start: 0.7844 (tp) cc_final: 0.7631 (mm) REVERT: K 485 SER cc_start: 0.7064 (t) cc_final: 0.6522 (p) REVERT: K 501 GLN cc_start: 0.6941 (mt0) cc_final: 0.6576 (mt0) REVERT: K 503 ASP cc_start: 0.6895 (OUTLIER) cc_final: 0.5326 (m-30) REVERT: L 317 ASP cc_start: 0.7461 (m-30) cc_final: 0.7225 (m-30) REVERT: M 40 ASP cc_start: 0.8293 (t70) cc_final: 0.8087 (t70) REVERT: M 391 THR cc_start: 0.6244 (m) cc_final: 0.5833 (p) REVERT: N 85 MET cc_start: 0.8801 (mtm) cc_final: 0.8126 (mtm) REVERT: N 102 LYS cc_start: 0.8000 (mttt) cc_final: 0.7671 (mtpp) REVERT: N 104 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.6830 (m-10) REVERT: N 170 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8454 (mp10) REVERT: N 293 VAL cc_start: 0.8319 (t) cc_final: 0.8014 (t) REVERT: N 329 SER cc_start: 0.8300 (t) cc_final: 0.7858 (m) REVERT: N 551 GLN cc_start: 0.8485 (mt0) cc_final: 0.8272 (mt0) REVERT: N 553 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8393 (tt) REVERT: O 122 LYS cc_start: 0.6902 (tttt) cc_final: 0.6296 (tmtt) REVERT: Q 173 ASP cc_start: 0.6972 (m-30) cc_final: 0.6599 (t0) REVERT: Q 203 MET cc_start: 0.8732 (mmt) cc_final: 0.8357 (mmt) REVERT: Q 266 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7333 (pt0) REVERT: Q 294 ASP cc_start: 0.7805 (t0) cc_final: 0.7351 (t0) REVERT: Q 303 LYS cc_start: 0.8529 (mttt) cc_final: 0.8305 (mmtt) REVERT: R 193 ILE cc_start: 0.8099 (mt) cc_final: 0.7825 (pt) REVERT: R 306 GLU cc_start: 0.6363 (mt-10) cc_final: 0.6040 (pt0) REVERT: S 218 ASN cc_start: 0.6751 (m-40) cc_final: 0.6270 (t0) outliers start: 64 outliers final: 16 residues processed: 729 average time/residue: 0.4265 time to fit residues: 472.9804 Evaluate side-chains 407 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 385 time to evaluate : 3.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 281 ASN Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain K residue 503 ASP Chi-restraints excluded: chain M residue 316 ASP Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 170 GLN Chi-restraints excluded: chain N residue 553 ILE Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain Q residue 342 ASP Chi-restraints excluded: chain Q residue 345 ASP Chi-restraints excluded: chain Q residue 368 ASP Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 262 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.2980 chunk 231 optimal weight: 0.9980 chunk 128 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 277 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 HIS D 64 HIS D 108 HIS D 122 HIS E 331 ASN E 425 GLN E 432 ASN F 816 ASN F 855 ASN H 452 GLN ** H 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 494 ASN H 506 GLN H 514 HIS H 529 ASN H 601 HIS ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 253 GLN I 314 ASN K 426 GLN K 430 GLN ** K 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 145 ASN ** L 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 318 GLN M 340 ASN ** M 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 43 GLN N 69 GLN N 286 HIS N 512 ASN N 559 HIS ** N 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN O 22 ASN O 97 HIS O 193 GLN ** O 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 482 ASN O 484 ASN Q 5 ASN Q 158 GLN Q 164 ASN Q 220 GLN Q 261 GLN Q 295 ASN Q 352 HIS R 57 GLN R 116 ASN R 123 GLN R 204 ASN R 270 HIS R 290 GLN S 227 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 25543 Z= 0.196 Angle : 0.549 14.690 34555 Z= 0.279 Chirality : 0.040 0.238 3971 Planarity : 0.004 0.073 4440 Dihedral : 5.254 59.880 3399 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.91 % Favored : 94.06 % Rotamer: Outliers : 3.03 % Allowed : 11.24 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 2946 helix: 1.61 (0.13), residues: 1531 sheet: -0.45 (0.35), residues: 186 loop : -2.34 (0.16), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 273 HIS 0.005 0.001 HIS N 220 PHE 0.028 0.001 PHE R 83 TYR 0.019 0.001 TYR O 178 ARG 0.006 0.000 ARG O 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 397 time to evaluate : 3.253 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: C 48 ARG cc_start: 0.7559 (ttt90) cc_final: 0.7116 (tmt170) REVERT: C 64 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7390 (tp30) REVERT: D 94 ARG cc_start: 0.6861 (ttt180) cc_final: 0.6617 (ttt-90) REVERT: D 107 HIS cc_start: 0.7427 (t70) cc_final: 0.7076 (t-90) REVERT: E 329 ARG cc_start: 0.7596 (mtm110) cc_final: 0.6488 (mmt180) REVERT: E 407 LYS cc_start: 0.7179 (pttp) cc_final: 0.6899 (ptmm) REVERT: F 817 ARG cc_start: 0.6932 (mtp180) cc_final: 0.6406 (mtp85) REVERT: G 167 MET cc_start: 0.8260 (ttm) cc_final: 0.7558 (mtp) REVERT: G 176 GLU cc_start: 0.3310 (OUTLIER) cc_final: 0.2486 (tt0) REVERT: H 446 LYS cc_start: 0.8265 (ttmm) cc_final: 0.8035 (ttmm) REVERT: H 589 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6722 (mt-10) REVERT: I 63 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7991 (mm-40) REVERT: I 239 GLN cc_start: 0.7885 (mp10) cc_final: 0.7677 (mp10) REVERT: I 281 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8608 (m-40) REVERT: I 312 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7547 (tptt) REVERT: I 317 ASP cc_start: 0.7622 (m-30) cc_final: 0.7300 (m-30) REVERT: J 388 LYS cc_start: 0.7789 (mttt) cc_final: 0.7498 (mppt) REVERT: J 395 ASP cc_start: 0.8334 (m-30) cc_final: 0.8031 (m-30) REVERT: J 437 MET cc_start: 0.7678 (mmm) cc_final: 0.7149 (mmt) REVERT: J 463 LYS cc_start: 0.7898 (mmmt) cc_final: 0.7453 (mmmt) REVERT: L 104 ASP cc_start: 0.7057 (OUTLIER) cc_final: 0.6547 (t70) REVERT: L 149 ASP cc_start: 0.7266 (p0) cc_final: 0.7024 (p0) REVERT: L 240 ASP cc_start: 0.8099 (m-30) cc_final: 0.7867 (m-30) REVERT: L 312 LYS cc_start: 0.7096 (mttt) cc_final: 0.6456 (tptt) REVERT: L 317 ASP cc_start: 0.7912 (m-30) cc_final: 0.7602 (m-30) REVERT: M 468 ARG cc_start: 0.7218 (mmm-85) cc_final: 0.6207 (mpt180) REVERT: N 85 MET cc_start: 0.8696 (mtm) cc_final: 0.8338 (mtm) REVERT: N 102 LYS cc_start: 0.8019 (mttt) cc_final: 0.7702 (mtpp) REVERT: N 104 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.7119 (m-80) REVERT: N 170 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8577 (mp10) REVERT: N 293 VAL cc_start: 0.8127 (t) cc_final: 0.7863 (t) REVERT: N 553 ILE cc_start: 0.8536 (tt) cc_final: 0.8117 (tp) REVERT: O 122 LYS cc_start: 0.6948 (tttt) cc_final: 0.6336 (tmtt) REVERT: O 265 MET cc_start: 0.8176 (mtt) cc_final: 0.7586 (mtt) REVERT: Q 173 ASP cc_start: 0.6998 (m-30) cc_final: 0.6786 (t0) REVERT: Q 294 ASP cc_start: 0.7750 (t0) cc_final: 0.7213 (t0) REVERT: Q 303 LYS cc_start: 0.8453 (mttt) cc_final: 0.8178 (mmtt) REVERT: Q 341 LYS cc_start: 0.7462 (mtpp) cc_final: 0.7162 (tptp) REVERT: Q 343 TRP cc_start: 0.7982 (t60) cc_final: 0.7650 (t60) REVERT: R 101 ARG cc_start: 0.7556 (ttm-80) cc_final: 0.7211 (mtt90) REVERT: R 102 LYS cc_start: 0.7972 (ptmm) cc_final: 0.7583 (mmtm) REVERT: R 234 MET cc_start: 0.8636 (mmm) cc_final: 0.7247 (mmm) REVERT: R 306 GLU cc_start: 0.6380 (mt-10) cc_final: 0.6075 (pt0) REVERT: S 218 ASN cc_start: 0.6607 (m-40) cc_final: 0.6169 (t0) outliers start: 84 outliers final: 44 residues processed: 457 average time/residue: 0.4082 time to fit residues: 289.1836 Evaluate side-chains 394 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 343 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 237 SER Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 281 ASN Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain J residue 452 THR Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 104 ASP Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 244 MET Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 170 GLN Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 285 ASP Chi-restraints excluded: chain N residue 321 GLN Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 357 GLN Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain N residue 578 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 412 ASN Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 268 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain S residue 213 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 278 optimal weight: 4.9990 chunk 300 optimal weight: 20.0000 chunk 247 optimal weight: 4.9990 chunk 276 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 223 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 23 GLN D 122 HIS ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 HIS ** H 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 496 ASN H 506 GLN H 512 GLN I 60 GLN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 255 HIS M 378 GLN M 380 GLN N 551 GLN N 577 ASN O 97 HIS O 234 GLN ** Q 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 123 GLN S 227 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 25543 Z= 0.280 Angle : 0.579 13.969 34555 Z= 0.296 Chirality : 0.042 0.215 3971 Planarity : 0.004 0.076 4440 Dihedral : 5.099 57.247 3379 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.94 % Favored : 94.03 % Rotamer: Outliers : 3.28 % Allowed : 12.25 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 2946 helix: 1.93 (0.13), residues: 1524 sheet: -0.18 (0.36), residues: 181 loop : -2.09 (0.16), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP O 273 HIS 0.006 0.001 HIS Q 3 PHE 0.027 0.002 PHE R 83 TYR 0.025 0.002 TYR Q 225 ARG 0.007 0.001 ARG I 249 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 380 time to evaluate : 3.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 ARG cc_start: 0.7501 (ttt90) cc_final: 0.7087 (tmt170) REVERT: D 107 HIS cc_start: 0.7735 (t70) cc_final: 0.7389 (t-90) REVERT: E 329 ARG cc_start: 0.7505 (mtm110) cc_final: 0.6322 (mmt180) REVERT: E 387 GLU cc_start: 0.8655 (pt0) cc_final: 0.8369 (pt0) REVERT: E 407 LYS cc_start: 0.7206 (pttp) cc_final: 0.6976 (ptmm) REVERT: E 420 ARG cc_start: 0.7424 (mtp180) cc_final: 0.6870 (ttp80) REVERT: F 817 ARG cc_start: 0.6929 (mtp180) cc_final: 0.6270 (mtp85) REVERT: G 167 MET cc_start: 0.8101 (ttm) cc_final: 0.7699 (mtp) REVERT: H 613 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7344 (mt-10) REVERT: I 281 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8631 (m-40) REVERT: I 312 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7540 (tptt) REVERT: I 317 ASP cc_start: 0.7847 (m-30) cc_final: 0.7591 (m-30) REVERT: I 346 ARG cc_start: 0.6775 (mtp85) cc_final: 0.6523 (mtp85) REVERT: I 360 GLU cc_start: 0.8183 (tt0) cc_final: 0.7939 (tt0) REVERT: J 388 LYS cc_start: 0.7880 (mttt) cc_final: 0.7509 (mppt) REVERT: J 395 ASP cc_start: 0.8288 (m-30) cc_final: 0.7941 (m-30) REVERT: K 468 MET cc_start: 0.6912 (tmm) cc_final: 0.6696 (tmm) REVERT: K 501 GLN cc_start: 0.7239 (mt0) cc_final: 0.6938 (mt0) REVERT: L 66 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7214 (mt-10) REVERT: L 104 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6624 (t70) REVERT: L 149 ASP cc_start: 0.7359 (p0) cc_final: 0.6782 (p0) REVERT: L 312 LYS cc_start: 0.7076 (mttt) cc_final: 0.6294 (tptt) REVERT: L 317 ASP cc_start: 0.7956 (m-30) cc_final: 0.7735 (m-30) REVERT: M 445 GLN cc_start: 0.7886 (pt0) cc_final: 0.7428 (pp30) REVERT: M 468 ARG cc_start: 0.7231 (mmm-85) cc_final: 0.6298 (mpt180) REVERT: N 104 TYR cc_start: 0.9169 (OUTLIER) cc_final: 0.7530 (m-80) REVERT: N 170 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8342 (mp10) REVERT: N 553 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8380 (tp) REVERT: O 48 TYR cc_start: 0.6891 (t80) cc_final: 0.6658 (t80) REVERT: O 80 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.7170 (t80) REVERT: O 122 LYS cc_start: 0.7054 (tttt) cc_final: 0.6438 (tmtt) REVERT: O 129 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7513 (pt0) REVERT: O 265 MET cc_start: 0.8147 (mtt) cc_final: 0.7567 (mtt) REVERT: Q 203 MET cc_start: 0.8645 (mmt) cc_final: 0.8394 (mmt) REVERT: Q 303 LYS cc_start: 0.8560 (mttt) cc_final: 0.8169 (mmtt) REVERT: R 50 ARG cc_start: 0.6864 (ttt90) cc_final: 0.6614 (mtp-110) REVERT: R 108 PHE cc_start: 0.6623 (t80) cc_final: 0.6397 (t80) REVERT: R 134 TYR cc_start: 0.6977 (p90) cc_final: 0.6686 (p90) REVERT: R 234 MET cc_start: 0.8714 (mmm) cc_final: 0.7447 (mmm) REVERT: R 306 GLU cc_start: 0.6261 (mt-10) cc_final: 0.5963 (pt0) REVERT: S 218 ASN cc_start: 0.6555 (m-40) cc_final: 0.6098 (t0) outliers start: 91 outliers final: 63 residues processed: 441 average time/residue: 0.4561 time to fit residues: 310.2600 Evaluate side-chains 403 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 333 time to evaluate : 3.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain F residue 798 ILE Chi-restraints excluded: chain F residue 800 ASN Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain H residue 451 ILE Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 530 LYS Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 237 SER Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 281 ASN Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain J residue 452 THR Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain L residue 104 ASP Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 170 GLN Chi-restraints excluded: chain N residue 173 ASP Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 285 ASP Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 357 GLN Chi-restraints excluded: chain N residue 553 ILE Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain N residue 577 ASN Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 29 HIS Chi-restraints excluded: chain O residue 80 PHE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 279 THR Chi-restraints excluded: chain O residue 412 ASN Chi-restraints excluded: chain Q residue 207 THR Chi-restraints excluded: chain Q residue 268 ILE Chi-restraints excluded: chain Q residue 344 VAL Chi-restraints excluded: chain Q residue 376 TRP Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain S residue 198 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 0.7980 chunk 209 optimal weight: 9.9990 chunk 144 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 132 optimal weight: 0.1980 chunk 186 optimal weight: 0.6980 chunk 279 optimal weight: 0.9980 chunk 295 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 264 optimal weight: 0.0470 chunk 79 optimal weight: 0.8980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 HIS ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 GLN H 493 GLN H 506 GLN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 394 ASN K 430 GLN ** N 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 HIS O 234 GLN O 484 ASN Q 297 GLN S 227 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25543 Z= 0.146 Angle : 0.498 13.874 34555 Z= 0.254 Chirality : 0.038 0.164 3971 Planarity : 0.004 0.073 4440 Dihedral : 4.818 55.733 3377 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.43 % Favored : 94.53 % Rotamer: Outliers : 2.74 % Allowed : 13.72 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.16), residues: 2946 helix: 2.36 (0.13), residues: 1519 sheet: 0.07 (0.37), residues: 183 loop : -1.90 (0.16), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 273 HIS 0.003 0.001 HIS N 220 PHE 0.017 0.001 PHE R 83 TYR 0.025 0.001 TYR R 93 ARG 0.004 0.000 ARG R 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 357 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 48 ARG cc_start: 0.7602 (ttt90) cc_final: 0.7133 (tmt170) REVERT: D 107 HIS cc_start: 0.7725 (t70) cc_final: 0.7369 (t-90) REVERT: E 329 ARG cc_start: 0.7618 (mtm110) cc_final: 0.6445 (mmt180) REVERT: E 407 LYS cc_start: 0.7353 (pttp) cc_final: 0.7104 (ptmm) REVERT: E 420 ARG cc_start: 0.7512 (mtp180) cc_final: 0.7059 (ttp80) REVERT: F 817 ARG cc_start: 0.6848 (mtp180) cc_final: 0.6170 (mtp85) REVERT: G 176 GLU cc_start: 0.3184 (OUTLIER) cc_final: 0.2348 (tt0) REVERT: H 531 GLU cc_start: 0.7924 (mp0) cc_final: 0.7523 (tp30) REVERT: I 191 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8518 (pp) REVERT: I 281 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8633 (m-40) REVERT: I 312 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7350 (pttt) REVERT: I 317 ASP cc_start: 0.7868 (m-30) cc_final: 0.7565 (m-30) REVERT: J 388 LYS cc_start: 0.7876 (mttt) cc_final: 0.7498 (mppt) REVERT: J 395 ASP cc_start: 0.8291 (m-30) cc_final: 0.7932 (m-30) REVERT: K 468 MET cc_start: 0.7008 (tmm) cc_final: 0.6802 (tmm) REVERT: K 499 SER cc_start: 0.7914 (m) cc_final: 0.7115 (p) REVERT: K 501 GLN cc_start: 0.7117 (mt0) cc_final: 0.6881 (mt0) REVERT: L 66 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6839 (mt-10) REVERT: L 95 HIS cc_start: 0.7112 (t-90) cc_final: 0.6896 (t-90) REVERT: L 104 ASP cc_start: 0.7058 (OUTLIER) cc_final: 0.5861 (t70) REVERT: L 149 ASP cc_start: 0.7307 (p0) cc_final: 0.6694 (p0) REVERT: L 240 ASP cc_start: 0.8266 (m-30) cc_final: 0.8016 (m-30) REVERT: L 312 LYS cc_start: 0.7077 (mttt) cc_final: 0.6265 (tptt) REVERT: M 445 GLN cc_start: 0.7709 (pt0) cc_final: 0.7316 (pp30) REVERT: M 468 ARG cc_start: 0.7154 (mmm-85) cc_final: 0.6235 (mpt180) REVERT: N 28 MET cc_start: 0.5348 (tmm) cc_final: 0.4702 (tmm) REVERT: N 104 TYR cc_start: 0.9228 (OUTLIER) cc_final: 0.7706 (m-80) REVERT: N 293 VAL cc_start: 0.8162 (t) cc_final: 0.7792 (t) REVERT: N 310 ASP cc_start: 0.8110 (m-30) cc_final: 0.7804 (m-30) REVERT: N 553 ILE cc_start: 0.8538 (tt) cc_final: 0.8126 (tp) REVERT: O 80 PHE cc_start: 0.7447 (OUTLIER) cc_final: 0.7228 (t80) REVERT: O 122 LYS cc_start: 0.7028 (tttt) cc_final: 0.6382 (tmtt) REVERT: O 129 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7503 (pt0) REVERT: Q 272 GLU cc_start: 0.7050 (pm20) cc_final: 0.6539 (pm20) REVERT: Q 294 ASP cc_start: 0.7827 (t0) cc_final: 0.7551 (t0) REVERT: Q 303 LYS cc_start: 0.8576 (mttt) cc_final: 0.8163 (mmtt) REVERT: R 50 ARG cc_start: 0.6891 (ttt90) cc_final: 0.6606 (mtp-110) REVERT: R 134 TYR cc_start: 0.6961 (p90) cc_final: 0.6630 (p90) REVERT: R 259 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.7760 (pt0) REVERT: R 306 GLU cc_start: 0.5954 (mt-10) cc_final: 0.5635 (pt0) REVERT: S 218 ASN cc_start: 0.6550 (m-40) cc_final: 0.6100 (t0) outliers start: 76 outliers final: 49 residues processed: 408 average time/residue: 0.4084 time to fit residues: 257.8196 Evaluate side-chains 395 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 338 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 530 LYS Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 237 SER Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 281 ASN Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain J residue 486 LEU Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 104 ASP Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 244 MET Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 173 ASP Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 285 ASP Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain N residue 577 ASN Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 80 PHE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain S residue 211 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 220 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 252 optimal weight: 0.8980 chunk 204 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 151 optimal weight: 0.0030 chunk 265 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 23 GLN D 122 HIS ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 493 GLN H 506 GLN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 394 ASN ** N 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 577 ASN O 97 HIS Q 297 GLN S 227 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25543 Z= 0.191 Angle : 0.511 13.778 34555 Z= 0.260 Chirality : 0.039 0.174 3971 Planarity : 0.004 0.074 4440 Dihedral : 4.602 53.481 3374 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.63 % Favored : 94.33 % Rotamer: Outliers : 3.03 % Allowed : 14.30 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: 1.00 (0.16), residues: 2946 helix: 2.51 (0.13), residues: 1515 sheet: 0.13 (0.37), residues: 189 loop : -1.75 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 273 HIS 0.004 0.001 HIS O 97 PHE 0.015 0.001 PHE I 85 TYR 0.014 0.001 TYR Q 225 ARG 0.010 0.000 ARG R 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 364 time to evaluate : 3.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 ARG cc_start: 0.7608 (ttt90) cc_final: 0.7133 (tmt170) REVERT: C 63 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7439 (mm-30) REVERT: D 107 HIS cc_start: 0.7787 (t70) cc_final: 0.7443 (t-90) REVERT: E 329 ARG cc_start: 0.7662 (mtm110) cc_final: 0.6459 (mmt180) REVERT: E 407 LYS cc_start: 0.7378 (pttp) cc_final: 0.7130 (ptmm) REVERT: F 817 ARG cc_start: 0.6856 (mtp180) cc_final: 0.6048 (mtp85) REVERT: G 176 GLU cc_start: 0.3247 (OUTLIER) cc_final: 0.2398 (tt0) REVERT: H 531 GLU cc_start: 0.7949 (mp0) cc_final: 0.7572 (tp30) REVERT: I 63 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7813 (mm-40) REVERT: I 191 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8556 (pp) REVERT: I 281 ASN cc_start: 0.8871 (OUTLIER) cc_final: 0.8659 (m-40) REVERT: I 312 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7364 (pttt) REVERT: J 388 LYS cc_start: 0.7904 (mttt) cc_final: 0.7508 (mppt) REVERT: J 395 ASP cc_start: 0.8220 (m-30) cc_final: 0.7848 (m-30) REVERT: K 499 SER cc_start: 0.7841 (m) cc_final: 0.7005 (p) REVERT: K 501 GLN cc_start: 0.7044 (mt0) cc_final: 0.6820 (mt0) REVERT: L 66 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6711 (mt-10) REVERT: L 94 ILE cc_start: 0.7699 (mm) cc_final: 0.7347 (mm) REVERT: L 95 HIS cc_start: 0.7039 (t-90) cc_final: 0.6832 (t-90) REVERT: L 149 ASP cc_start: 0.7341 (p0) cc_final: 0.6706 (p0) REVERT: L 312 LYS cc_start: 0.7093 (mttt) cc_final: 0.6258 (tptt) REVERT: M 445 GLN cc_start: 0.7719 (pt0) cc_final: 0.7391 (pp30) REVERT: N 28 MET cc_start: 0.5321 (tmm) cc_final: 0.4994 (tmm) REVERT: N 104 TYR cc_start: 0.9227 (OUTLIER) cc_final: 0.7700 (m-80) REVERT: N 310 ASP cc_start: 0.8139 (m-30) cc_final: 0.7820 (m-30) REVERT: N 553 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8148 (tp) REVERT: O 48 TYR cc_start: 0.6410 (t80) cc_final: 0.5825 (t80) REVERT: O 122 LYS cc_start: 0.6642 (tttt) cc_final: 0.6104 (tmtt) REVERT: O 129 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7490 (pt0) REVERT: Q 272 GLU cc_start: 0.7120 (pm20) cc_final: 0.6891 (pm20) REVERT: Q 294 ASP cc_start: 0.7918 (t0) cc_final: 0.7646 (t0) REVERT: Q 303 LYS cc_start: 0.8604 (mttt) cc_final: 0.8121 (mmtt) REVERT: R 50 ARG cc_start: 0.7052 (ttt90) cc_final: 0.6721 (mtp-110) REVERT: R 229 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7440 (t0) REVERT: R 259 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.7799 (pt0) REVERT: R 306 GLU cc_start: 0.6184 (mt-10) cc_final: 0.5829 (pt0) REVERT: S 218 ASN cc_start: 0.6560 (m-40) cc_final: 0.6146 (t0) outliers start: 84 outliers final: 57 residues processed: 415 average time/residue: 0.3982 time to fit residues: 258.4666 Evaluate side-chains 414 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 349 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain F residue 798 ILE Chi-restraints excluded: chain F residue 800 ASN Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 237 SER Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 281 ASN Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 173 ASP Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 285 ASP Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 553 ILE Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain N residue 577 ASN Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 176 ILE Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 296 GLU Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 229 ASP Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain S residue 211 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 6.9990 chunk 266 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 173 optimal weight: 0.0270 chunk 73 optimal weight: 1.9990 chunk 296 optimal weight: 9.9990 chunk 245 optimal weight: 0.9980 chunk 137 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 HIS E 331 ASN F 855 ASN ** H 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 506 GLN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 394 ASN M 61 ASN ** N 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 577 ASN O 97 HIS Q 297 GLN Q 352 HIS S 227 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25543 Z= 0.160 Angle : 0.498 13.654 34555 Z= 0.253 Chirality : 0.038 0.154 3971 Planarity : 0.003 0.072 4440 Dihedral : 4.502 51.042 3374 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.47 % Favored : 94.50 % Rotamer: Outliers : 2.88 % Allowed : 15.27 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: 1.18 (0.16), residues: 2946 helix: 2.67 (0.13), residues: 1506 sheet: 0.16 (0.37), residues: 191 loop : -1.63 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 319 HIS 0.004 0.001 HIS O 97 PHE 0.013 0.001 PHE O 35 TYR 0.016 0.001 TYR O 178 ARG 0.009 0.000 ARG R 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 367 time to evaluate : 3.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 ARG cc_start: 0.7689 (ttt90) cc_final: 0.7213 (tmt170) REVERT: C 63 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7475 (mm-30) REVERT: D 107 HIS cc_start: 0.7796 (t70) cc_final: 0.7456 (t-90) REVERT: E 329 ARG cc_start: 0.7440 (mtm110) cc_final: 0.6175 (mmt180) REVERT: E 407 LYS cc_start: 0.7349 (pttp) cc_final: 0.6930 (ptmm) REVERT: F 817 ARG cc_start: 0.6820 (mtp180) cc_final: 0.6007 (mtp85) REVERT: G 176 GLU cc_start: 0.3158 (OUTLIER) cc_final: 0.2355 (tt0) REVERT: H 531 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7598 (tp30) REVERT: I 63 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7832 (mm-40) REVERT: I 170 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8550 (tt) REVERT: I 191 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8526 (pp) REVERT: J 388 LYS cc_start: 0.7901 (mttt) cc_final: 0.7495 (mppt) REVERT: K 499 SER cc_start: 0.7564 (m) cc_final: 0.6739 (p) REVERT: K 501 GLN cc_start: 0.6964 (mt0) cc_final: 0.6752 (mt0) REVERT: L 94 ILE cc_start: 0.7592 (mm) cc_final: 0.7242 (mm) REVERT: L 149 ASP cc_start: 0.7441 (p0) cc_final: 0.6781 (p0) REVERT: L 312 LYS cc_start: 0.7101 (mttt) cc_final: 0.6262 (tptt) REVERT: M 445 GLN cc_start: 0.7715 (pt0) cc_final: 0.7379 (pp30) REVERT: N 104 TYR cc_start: 0.9217 (OUTLIER) cc_final: 0.7667 (m-80) REVERT: N 114 MET cc_start: 0.7787 (mtp) cc_final: 0.7503 (mtp) REVERT: N 293 VAL cc_start: 0.8178 (t) cc_final: 0.7788 (t) REVERT: N 310 ASP cc_start: 0.8143 (m-30) cc_final: 0.7833 (m-30) REVERT: N 553 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8106 (tp) REVERT: O 48 TYR cc_start: 0.6355 (t80) cc_final: 0.5818 (t80) REVERT: O 122 LYS cc_start: 0.6641 (tttt) cc_final: 0.6109 (tmtt) REVERT: O 129 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7503 (pt0) REVERT: O 202 MET cc_start: 0.7397 (pmm) cc_final: 0.6708 (ptm) REVERT: Q 272 GLU cc_start: 0.7208 (pm20) cc_final: 0.6985 (pm20) REVERT: Q 294 ASP cc_start: 0.7866 (t0) cc_final: 0.7572 (t0) REVERT: Q 303 LYS cc_start: 0.8613 (mttt) cc_final: 0.8111 (mmtt) REVERT: R 50 ARG cc_start: 0.6956 (ttt90) cc_final: 0.6609 (mtp-110) REVERT: R 83 PHE cc_start: 0.8852 (m-80) cc_final: 0.8442 (m-80) REVERT: R 229 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7443 (t0) REVERT: R 234 MET cc_start: 0.8764 (tpp) cc_final: 0.8521 (tpp) REVERT: R 259 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.7798 (pt0) REVERT: R 261 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8609 (tp) REVERT: R 306 GLU cc_start: 0.6178 (mt-10) cc_final: 0.5823 (pt0) REVERT: S 218 ASN cc_start: 0.6562 (m-40) cc_final: 0.6121 (t0) outliers start: 80 outliers final: 53 residues processed: 417 average time/residue: 0.3951 time to fit residues: 258.3572 Evaluate side-chains 414 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 352 time to evaluate : 3.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain F residue 811 LEU Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 531 GLU Chi-restraints excluded: chain H residue 589 GLU Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain J residue 486 LEU Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 173 ASP Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 285 ASP Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 357 GLN Chi-restraints excluded: chain N residue 553 ILE Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 80 PHE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 229 ASP Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain S residue 211 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 216 optimal weight: 0.3980 chunk 167 optimal weight: 0.9980 chunk 249 optimal weight: 6.9990 chunk 165 optimal weight: 0.8980 chunk 294 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 136 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 HIS F 855 ASN ** H 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 506 GLN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 394 ASN K 394 ASN ** N 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 577 ASN O 97 HIS O 196 GLN Q 352 HIS ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 227 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25543 Z= 0.157 Angle : 0.494 13.021 34555 Z= 0.251 Chirality : 0.038 0.150 3971 Planarity : 0.003 0.069 4440 Dihedral : 4.427 49.873 3372 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.57 % Favored : 94.40 % Rotamer: Outliers : 2.85 % Allowed : 15.42 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: 1.31 (0.16), residues: 2946 helix: 2.76 (0.13), residues: 1507 sheet: 0.23 (0.37), residues: 185 loop : -1.54 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 273 HIS 0.004 0.001 HIS Q 352 PHE 0.012 0.001 PHE O 35 TYR 0.015 0.001 TYR Q 225 ARG 0.007 0.000 ARG R 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 374 time to evaluate : 2.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 ARG cc_start: 0.7578 (ttt90) cc_final: 0.7161 (tmt170) REVERT: C 59 ARG cc_start: 0.7814 (ttp-110) cc_final: 0.7567 (ttp-110) REVERT: C 63 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7579 (mm-30) REVERT: D 107 HIS cc_start: 0.7812 (t70) cc_final: 0.7469 (t-90) REVERT: E 329 ARG cc_start: 0.7447 (mtm110) cc_final: 0.6181 (mmt180) REVERT: F 817 ARG cc_start: 0.6806 (mtp180) cc_final: 0.5979 (mtp85) REVERT: G 176 GLU cc_start: 0.3088 (OUTLIER) cc_final: 0.2335 (tt0) REVERT: H 531 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7646 (tp30) REVERT: I 63 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7825 (mm-40) REVERT: I 191 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8491 (pp) REVERT: I 312 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7494 (pttt) REVERT: J 388 LYS cc_start: 0.7897 (mttt) cc_final: 0.7420 (mppt) REVERT: K 499 SER cc_start: 0.7778 (OUTLIER) cc_final: 0.6998 (p) REVERT: K 501 GLN cc_start: 0.7092 (mt0) cc_final: 0.6832 (mt0) REVERT: L 94 ILE cc_start: 0.7575 (mm) cc_final: 0.7309 (mm) REVERT: L 148 MET cc_start: 0.8324 (mtp) cc_final: 0.8044 (mtp) REVERT: L 149 ASP cc_start: 0.7441 (p0) cc_final: 0.6750 (p0) REVERT: L 312 LYS cc_start: 0.7114 (mttt) cc_final: 0.6268 (tptt) REVERT: M 445 GLN cc_start: 0.7723 (pt0) cc_final: 0.7399 (pp30) REVERT: N 104 TYR cc_start: 0.9217 (OUTLIER) cc_final: 0.7721 (m-80) REVERT: N 290 SER cc_start: 0.8808 (t) cc_final: 0.8486 (m) REVERT: N 293 VAL cc_start: 0.8171 (t) cc_final: 0.7787 (t) REVERT: N 310 ASP cc_start: 0.8140 (m-30) cc_final: 0.7812 (m-30) REVERT: N 553 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8071 (tp) REVERT: O 48 TYR cc_start: 0.6092 (t80) cc_final: 0.5573 (t80) REVERT: O 122 LYS cc_start: 0.6682 (tttt) cc_final: 0.6157 (tmtt) REVERT: O 129 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7498 (pt0) REVERT: Q 294 ASP cc_start: 0.7834 (t0) cc_final: 0.7507 (t0) REVERT: Q 303 LYS cc_start: 0.8606 (mttt) cc_final: 0.8108 (mmtt) REVERT: R 50 ARG cc_start: 0.7003 (ttt90) cc_final: 0.6652 (mtp-110) REVERT: R 83 PHE cc_start: 0.8845 (m-80) cc_final: 0.8441 (m-80) REVERT: R 229 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7447 (t0) REVERT: R 234 MET cc_start: 0.8794 (tpp) cc_final: 0.8555 (tpp) REVERT: R 259 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7777 (pt0) REVERT: R 261 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8686 (tp) REVERT: R 306 GLU cc_start: 0.6170 (mt-10) cc_final: 0.5822 (pt0) REVERT: S 199 MET cc_start: 0.8606 (ptp) cc_final: 0.8245 (pmm) REVERT: S 218 ASN cc_start: 0.6553 (m-40) cc_final: 0.6126 (t0) outliers start: 79 outliers final: 53 residues processed: 420 average time/residue: 0.4014 time to fit residues: 261.6485 Evaluate side-chains 411 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 348 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain F residue 800 ASN Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain F residue 811 LEU Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 531 GLU Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain J residue 452 THR Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 499 SER Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain N residue 173 ASP Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 357 GLN Chi-restraints excluded: chain N residue 553 ILE Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain N residue 577 ASN Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 176 ILE Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 344 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 229 ASP Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain S residue 211 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 0.9990 chunk 117 optimal weight: 0.4980 chunk 176 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 57 optimal weight: 0.0570 chunk 187 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 231 optimal weight: 0.0060 chunk 268 optimal weight: 0.8980 overall best weight: 0.4714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 HIS H 506 GLN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 394 ASN K 478 GLN M 270 GLN ** N 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 577 ASN O 97 HIS O 484 ASN Q 352 HIS R 116 ASN S 227 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25543 Z= 0.137 Angle : 0.489 12.420 34555 Z= 0.248 Chirality : 0.038 0.200 3971 Planarity : 0.003 0.067 4440 Dihedral : 4.219 48.042 3368 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.13 % Favored : 94.84 % Rotamer: Outliers : 2.70 % Allowed : 16.21 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: 1.43 (0.16), residues: 2946 helix: 2.84 (0.13), residues: 1509 sheet: 0.24 (0.38), residues: 181 loop : -1.46 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 319 HIS 0.004 0.001 HIS O 97 PHE 0.028 0.001 PHE O 109 TYR 0.015 0.001 TYR Q 225 ARG 0.008 0.000 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 366 time to evaluate : 3.130 Fit side-chains revert: symmetry clash REVERT: C 38 GLU cc_start: 0.7932 (tp30) cc_final: 0.7628 (tp30) REVERT: C 48 ARG cc_start: 0.7566 (ttt90) cc_final: 0.7169 (tmt170) REVERT: C 59 ARG cc_start: 0.7797 (ttp-110) cc_final: 0.7537 (ttp-110) REVERT: C 63 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7594 (mm-30) REVERT: D 107 HIS cc_start: 0.7810 (t70) cc_final: 0.7473 (t-90) REVERT: E 329 ARG cc_start: 0.7429 (mtm110) cc_final: 0.6166 (mmt180) REVERT: F 817 ARG cc_start: 0.6873 (mtp180) cc_final: 0.5987 (mtp85) REVERT: G 176 GLU cc_start: 0.2952 (OUTLIER) cc_final: 0.2309 (tt0) REVERT: H 523 GLU cc_start: 0.6388 (mt-10) cc_final: 0.6167 (mt-10) REVERT: H 531 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7594 (tp30) REVERT: I 63 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7817 (mm-40) REVERT: I 183 PHE cc_start: 0.7343 (t80) cc_final: 0.6316 (p90) REVERT: I 191 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8454 (pp) REVERT: I 312 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7245 (pttt) REVERT: J 388 LYS cc_start: 0.7766 (mttt) cc_final: 0.7362 (mppt) REVERT: K 468 MET cc_start: 0.6918 (tmm) cc_final: 0.6686 (tmm) REVERT: K 499 SER cc_start: 0.7541 (OUTLIER) cc_final: 0.6745 (p) REVERT: L 94 ILE cc_start: 0.7437 (mm) cc_final: 0.7130 (mm) REVERT: L 149 ASP cc_start: 0.7300 (p0) cc_final: 0.6641 (p0) REVERT: L 312 LYS cc_start: 0.7144 (mttt) cc_final: 0.6245 (tptt) REVERT: M 445 GLN cc_start: 0.7700 (pt0) cc_final: 0.7380 (pp30) REVERT: N 28 MET cc_start: 0.5311 (tmm) cc_final: 0.4376 (tmm) REVERT: N 32 MET cc_start: 0.8406 (mtp) cc_final: 0.8134 (mtp) REVERT: N 290 SER cc_start: 0.8807 (t) cc_final: 0.8491 (m) REVERT: N 293 VAL cc_start: 0.8100 (t) cc_final: 0.7779 (t) REVERT: N 310 ASP cc_start: 0.8119 (m-30) cc_final: 0.7799 (m-30) REVERT: N 355 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7938 (tp) REVERT: N 553 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8112 (tp) REVERT: O 48 TYR cc_start: 0.6102 (t80) cc_final: 0.5616 (t80) REVERT: O 122 LYS cc_start: 0.6601 (tttt) cc_final: 0.6057 (tmtt) REVERT: O 129 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7488 (pt0) REVERT: Q 173 ASP cc_start: 0.7316 (m-30) cc_final: 0.7065 (t0) REVERT: Q 294 ASP cc_start: 0.7805 (t0) cc_final: 0.7471 (t0) REVERT: Q 303 LYS cc_start: 0.8612 (mttt) cc_final: 0.8109 (mmtt) REVERT: Q 379 ARG cc_start: 0.7832 (ptp90) cc_final: 0.7607 (ptp90) REVERT: R 50 ARG cc_start: 0.7015 (ttt90) cc_final: 0.6661 (mtp-110) REVERT: R 83 PHE cc_start: 0.8591 (m-80) cc_final: 0.8248 (m-80) REVERT: R 116 ASN cc_start: 0.7940 (OUTLIER) cc_final: 0.7706 (t0) REVERT: R 229 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7423 (t0) REVERT: R 234 MET cc_start: 0.8812 (tpp) cc_final: 0.8549 (tpp) REVERT: R 259 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7735 (pt0) REVERT: R 261 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8606 (tp) REVERT: S 198 LEU cc_start: 0.8342 (tt) cc_final: 0.8021 (tt) REVERT: S 218 ASN cc_start: 0.6533 (m-40) cc_final: 0.6121 (t0) outliers start: 75 outliers final: 52 residues processed: 416 average time/residue: 0.4010 time to fit residues: 258.7521 Evaluate side-chains 418 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 355 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain F residue 800 ASN Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 530 LYS Chi-restraints excluded: chain H residue 531 GLU Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain J residue 486 LEU Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 499 SER Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 147 CYS Chi-restraints excluded: chain N residue 173 ASP Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 285 ASP Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 357 GLN Chi-restraints excluded: chain N residue 553 ILE Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 80 PHE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 176 ILE Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 344 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 116 ASN Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 229 ASP Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain S residue 211 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 0.0980 chunk 257 optimal weight: 3.9990 chunk 274 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 215 optimal weight: 0.0980 chunk 84 optimal weight: 0.7980 chunk 248 optimal weight: 0.6980 chunk 259 optimal weight: 0.7980 chunk 273 optimal weight: 0.2980 chunk 180 optimal weight: 0.5980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 HIS H 506 GLN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 394 ASN K 501 GLN ** N 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 GLN O 97 HIS Q 352 HIS R 57 GLN S 227 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25543 Z= 0.131 Angle : 0.486 12.530 34555 Z= 0.247 Chirality : 0.038 0.190 3971 Planarity : 0.003 0.062 4440 Dihedral : 4.083 47.218 3366 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.26 % Favored : 94.70 % Rotamer: Outliers : 2.34 % Allowed : 16.61 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: 1.52 (0.16), residues: 2946 helix: 2.91 (0.13), residues: 1510 sheet: 0.28 (0.38), residues: 181 loop : -1.41 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 319 HIS 0.004 0.001 HIS O 97 PHE 0.025 0.001 PHE O 109 TYR 0.013 0.001 TYR L 272 ARG 0.009 0.000 ARG R 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 363 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 38 GLU cc_start: 0.7937 (tp30) cc_final: 0.7639 (tp30) REVERT: C 48 ARG cc_start: 0.7520 (ttt90) cc_final: 0.7116 (tmt170) REVERT: C 59 ARG cc_start: 0.7792 (ttp-110) cc_final: 0.7539 (ttp-110) REVERT: C 63 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7540 (mm-30) REVERT: D 107 HIS cc_start: 0.7810 (t70) cc_final: 0.7476 (t-90) REVERT: E 329 ARG cc_start: 0.7476 (mtm110) cc_final: 0.6233 (mmt180) REVERT: E 345 ASP cc_start: 0.7631 (m-30) cc_final: 0.7397 (m-30) REVERT: F 817 ARG cc_start: 0.6865 (mtp180) cc_final: 0.5939 (mtp85) REVERT: G 176 GLU cc_start: 0.2921 (OUTLIER) cc_final: 0.2284 (tt0) REVERT: H 523 GLU cc_start: 0.6384 (mt-10) cc_final: 0.6129 (mt-10) REVERT: H 531 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7593 (tp30) REVERT: H 613 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6676 (mm-30) REVERT: I 63 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7816 (mm-40) REVERT: I 312 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7266 (pttt) REVERT: J 388 LYS cc_start: 0.7749 (mttt) cc_final: 0.7349 (mppt) REVERT: K 499 SER cc_start: 0.7567 (OUTLIER) cc_final: 0.6748 (p) REVERT: L 94 ILE cc_start: 0.7483 (mm) cc_final: 0.7263 (mm) REVERT: L 149 ASP cc_start: 0.7268 (p0) cc_final: 0.6627 (p0) REVERT: L 312 LYS cc_start: 0.7155 (mttt) cc_final: 0.6248 (tptt) REVERT: M 445 GLN cc_start: 0.7764 (pt0) cc_final: 0.7461 (pp30) REVERT: N 28 MET cc_start: 0.5342 (tmm) cc_final: 0.4451 (tmm) REVERT: N 32 MET cc_start: 0.8301 (mtp) cc_final: 0.8012 (mtp) REVERT: N 35 ASN cc_start: 0.6454 (t0) cc_final: 0.6225 (t0) REVERT: N 104 TYR cc_start: 0.9213 (OUTLIER) cc_final: 0.7627 (m-80) REVERT: N 290 SER cc_start: 0.8813 (t) cc_final: 0.8503 (m) REVERT: N 293 VAL cc_start: 0.8078 (t) cc_final: 0.7762 (t) REVERT: N 310 ASP cc_start: 0.8109 (m-30) cc_final: 0.7766 (m-30) REVERT: N 355 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7962 (tp) REVERT: N 553 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8125 (tp) REVERT: O 48 TYR cc_start: 0.6065 (t80) cc_final: 0.5591 (t80) REVERT: O 122 LYS cc_start: 0.6481 (tttt) cc_final: 0.6007 (tmtt) REVERT: O 129 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7466 (pt0) REVERT: Q 173 ASP cc_start: 0.7340 (m-30) cc_final: 0.7055 (t0) REVERT: Q 294 ASP cc_start: 0.7792 (t0) cc_final: 0.7452 (t0) REVERT: Q 303 LYS cc_start: 0.8606 (mttt) cc_final: 0.8101 (mmtt) REVERT: Q 338 LYS cc_start: 0.7690 (ttmt) cc_final: 0.7476 (tptt) REVERT: Q 379 ARG cc_start: 0.7789 (ptp90) cc_final: 0.7580 (ptp90) REVERT: R 50 ARG cc_start: 0.7028 (ttt90) cc_final: 0.6666 (mtp-110) REVERT: R 83 PHE cc_start: 0.8570 (m-80) cc_final: 0.8215 (m-80) REVERT: R 229 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7397 (t0) REVERT: R 234 MET cc_start: 0.8839 (tpp) cc_final: 0.8571 (tpp) REVERT: R 259 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7709 (pt0) REVERT: R 261 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8606 (tp) REVERT: S 198 LEU cc_start: 0.8378 (tt) cc_final: 0.8108 (tt) REVERT: S 199 MET cc_start: 0.8484 (ptp) cc_final: 0.8228 (pmm) REVERT: S 218 ASN cc_start: 0.6524 (m-40) cc_final: 0.6133 (t0) outliers start: 65 outliers final: 47 residues processed: 406 average time/residue: 0.3949 time to fit residues: 251.0473 Evaluate side-chains 398 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 341 time to evaluate : 3.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 531 GLU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 499 SER Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain L residue 359 ILE Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain N residue 147 CYS Chi-restraints excluded: chain N residue 173 ASP Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 285 ASP Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 357 GLN Chi-restraints excluded: chain N residue 553 ILE Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 176 ILE Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 229 ASP Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain S residue 211 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 304 optimal weight: 20.0000 chunk 280 optimal weight: 4.9990 chunk 242 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 187 optimal weight: 4.9990 chunk 148 optimal weight: 0.0170 chunk 192 optimal weight: 0.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 HIS H 506 GLN H 618 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 394 ASN ** N 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 HIS O 186 ASN Q 3 HIS R 57 GLN ** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 227 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25543 Z= 0.166 Angle : 0.502 12.900 34555 Z= 0.254 Chirality : 0.039 0.181 3971 Planarity : 0.004 0.064 4440 Dihedral : 4.121 46.345 3366 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.26 % Favored : 94.70 % Rotamer: Outliers : 2.16 % Allowed : 16.79 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: 1.54 (0.16), residues: 2946 helix: 2.91 (0.13), residues: 1512 sheet: 0.36 (0.38), residues: 181 loop : -1.40 (0.17), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 319 HIS 0.004 0.001 HIS O 97 PHE 0.025 0.001 PHE O 109 TYR 0.015 0.001 TYR H 455 ARG 0.006 0.000 ARG D 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 352 time to evaluate : 3.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 38 GLU cc_start: 0.7945 (tp30) cc_final: 0.7658 (tp30) REVERT: C 48 ARG cc_start: 0.7584 (ttt90) cc_final: 0.7184 (tmt170) REVERT: C 59 ARG cc_start: 0.7754 (ttp-110) cc_final: 0.7454 (ttp-110) REVERT: D 107 HIS cc_start: 0.7836 (t70) cc_final: 0.7506 (t-90) REVERT: E 329 ARG cc_start: 0.7445 (mtm110) cc_final: 0.6158 (mmt180) REVERT: E 345 ASP cc_start: 0.7628 (m-30) cc_final: 0.7397 (m-30) REVERT: F 817 ARG cc_start: 0.6877 (mtp180) cc_final: 0.5938 (mtp85) REVERT: G 176 GLU cc_start: 0.2224 (OUTLIER) cc_final: 0.1614 (tt0) REVERT: H 523 GLU cc_start: 0.6441 (mt-10) cc_final: 0.6193 (mt-10) REVERT: H 531 GLU cc_start: 0.8114 (mp0) cc_final: 0.7732 (tp30) REVERT: H 613 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6581 (mm-30) REVERT: I 63 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7847 (mm-40) REVERT: I 312 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7170 (pttt) REVERT: J 388 LYS cc_start: 0.7633 (mttt) cc_final: 0.7265 (mppt) REVERT: K 499 SER cc_start: 0.7563 (OUTLIER) cc_final: 0.6750 (p) REVERT: L 94 ILE cc_start: 0.7455 (mm) cc_final: 0.7156 (mm) REVERT: L 312 LYS cc_start: 0.7173 (mttt) cc_final: 0.6259 (tptt) REVERT: M 445 GLN cc_start: 0.7719 (pt0) cc_final: 0.7404 (pp30) REVERT: N 28 MET cc_start: 0.5146 (tmm) cc_final: 0.4239 (tmm) REVERT: N 290 SER cc_start: 0.8909 (t) cc_final: 0.8606 (m) REVERT: N 293 VAL cc_start: 0.8228 (t) cc_final: 0.7878 (t) REVERT: N 310 ASP cc_start: 0.8143 (m-30) cc_final: 0.7794 (m-30) REVERT: N 355 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7985 (tp) REVERT: N 553 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8119 (tp) REVERT: O 48 TYR cc_start: 0.6060 (t80) cc_final: 0.5590 (t80) REVERT: O 122 LYS cc_start: 0.6659 (tttt) cc_final: 0.6077 (tmtt) REVERT: O 129 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7485 (pt0) REVERT: O 421 ASP cc_start: 0.7409 (t70) cc_final: 0.7209 (t0) REVERT: Q 294 ASP cc_start: 0.7789 (t0) cc_final: 0.7467 (t0) REVERT: Q 303 LYS cc_start: 0.8672 (mttt) cc_final: 0.8023 (mmtt) REVERT: Q 338 LYS cc_start: 0.7685 (ttmt) cc_final: 0.7467 (tptt) REVERT: Q 379 ARG cc_start: 0.7912 (ptp90) cc_final: 0.7695 (ptp90) REVERT: R 50 ARG cc_start: 0.7101 (ttt90) cc_final: 0.6759 (mtp-110) REVERT: R 97 LEU cc_start: 0.7847 (tt) cc_final: 0.7397 (tt) REVERT: R 101 ARG cc_start: 0.7595 (ttm-80) cc_final: 0.7297 (mtt90) REVERT: R 229 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7436 (t0) REVERT: R 234 MET cc_start: 0.8792 (tpp) cc_final: 0.8540 (tpp) REVERT: R 259 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7776 (pt0) REVERT: R 261 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8703 (tp) REVERT: S 198 LEU cc_start: 0.8249 (tt) cc_final: 0.8008 (tt) REVERT: S 199 MET cc_start: 0.8615 (ptp) cc_final: 0.8052 (pmm) REVERT: S 218 ASN cc_start: 0.6528 (m-40) cc_final: 0.6127 (t0) outliers start: 60 outliers final: 46 residues processed: 392 average time/residue: 0.3999 time to fit residues: 245.6566 Evaluate side-chains 396 residues out of total 2776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 342 time to evaluate : 3.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain F residue 800 ASN Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain I residue 366 GLU Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 499 SER Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain L residue 359 ILE Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 147 CYS Chi-restraints excluded: chain N residue 173 ASP Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 285 ASP Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 553 ILE Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 176 ILE Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 229 ASP Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain S residue 211 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 223 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 67 optimal weight: 0.0970 chunk 243 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 249 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 213 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 HIS H 506 GLN ** H 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 618 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 394 ASN K 501 GLN L 269 ASN ** N 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 GLN O 97 HIS O 186 ASN R 57 GLN S 227 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.158452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.113723 restraints weight = 36506.594| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.42 r_work: 0.3213 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25543 Z= 0.159 Angle : 0.508 13.423 34555 Z= 0.255 Chirality : 0.039 0.224 3971 Planarity : 0.004 0.066 4440 Dihedral : 4.110 45.478 3366 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 2.20 % Allowed : 16.97 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: 1.55 (0.16), residues: 2946 helix: 2.93 (0.13), residues: 1503 sheet: 0.35 (0.37), residues: 182 loop : -1.36 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 273 HIS 0.004 0.001 HIS O 97 PHE 0.049 0.001 PHE R 83 TYR 0.013 0.001 TYR O 117 ARG 0.006 0.000 ARG D 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6881.57 seconds wall clock time: 125 minutes 48.39 seconds (7548.39 seconds total)