Starting phenix.real_space_refine on Wed Mar 20 12:47:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w17_21502/03_2024/6w17_21502_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w17_21502/03_2024/6w17_21502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w17_21502/03_2024/6w17_21502.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w17_21502/03_2024/6w17_21502.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w17_21502/03_2024/6w17_21502_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w17_21502/03_2024/6w17_21502_updated.pdb" } resolution = 3.9 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 14 5.49 5 Mg 6 5.21 5 S 143 5.16 5 C 17319 2.51 5 N 4684 2.21 5 O 5230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A ASP 250": "OD1" <-> "OD2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "A ARG 352": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "B ARG 26": "NH1" <-> "NH2" Residue "B PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B ARG 116": "NH1" <-> "NH2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B ASP 179": "OD1" <-> "OD2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 380": "NH1" <-> "NH2" Residue "B ASP 383": "OD1" <-> "OD2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C ARG 242": "NH1" <-> "NH2" Residue "C ARG 255": "NH1" <-> "NH2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "D ASP 28": "OD1" <-> "OD2" Residue "D ASP 35": "OD1" <-> "OD2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D ARG 116": "NH1" <-> "NH2" Residue "D ARG 125": "NH1" <-> "NH2" Residue "D ARG 138": "NH1" <-> "NH2" Residue "D ASP 174": "OD1" <-> "OD2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D ARG 204": "NH1" <-> "NH2" Residue "D ARG 205": "NH1" <-> "NH2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D ASP 221": "OD1" <-> "OD2" Residue "D ASP 236": "OD1" <-> "OD2" Residue "D ARG 248": "NH1" <-> "NH2" Residue "D ARG 255": "NH1" <-> "NH2" Residue "D ARG 266": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F ARG 97": "NH1" <-> "NH2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F ARG 158": "NH1" <-> "NH2" Residue "G GLU 18": "OE1" <-> "OE2" Residue "G GLU 71": "OE1" <-> "OE2" Residue "G ASP 82": "OD1" <-> "OD2" Residue "G ARG 149": "NH1" <-> "NH2" Residue "H GLU 248": "OE1" <-> "OE2" Residue "H ARG 254": "NH1" <-> "NH2" Residue "H ASP 295": "OD1" <-> "OD2" Residue "H ASP 330": "OD1" <-> "OD2" Residue "H ARG 349": "NH1" <-> "NH2" Residue "I ARG 28": "NH1" <-> "NH2" Residue "I ARG 62": "NH1" <-> "NH2" Residue "I GLU 72": "OE1" <-> "OE2" Residue "I GLU 99": "OE1" <-> "OE2" Residue "I ARG 147": "NH1" <-> "NH2" Residue "I ARG 183": "NH1" <-> "NH2" Residue "I GLU 270": "OE1" <-> "OE2" Residue "I ARG 372": "NH1" <-> "NH2" Residue "J ARG 210": "NH1" <-> "NH2" Residue "J GLU 276": "OE1" <-> "OE2" Residue "J ARG 335": "NH1" <-> "NH2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "K ARG 183": "NH1" <-> "NH2" Residue "K ARG 210": "NH1" <-> "NH2" Residue "K ASP 292": "OD1" <-> "OD2" Residue "K ARG 335": "NH1" <-> "NH2" Residue "L ARG 28": "NH1" <-> "NH2" Residue "L ASP 81": "OD1" <-> "OD2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "L GLU 93": "OE1" <-> "OE2" Residue "L GLU 107": "OE1" <-> "OE2" Residue "L GLU 167": "OE1" <-> "OE2" Residue "L GLU 195": "OE1" <-> "OE2" Residue "L ASP 222": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27396 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2979 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 20, 'TRANS': 359} Chain breaks: 4 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2909 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 18, 'TRANS': 345} Chain breaks: 2 Chain: "C" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2589 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2435 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 285} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 861 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 12, 'TRANS': 161} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 736 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 8, 'ASN:plan1': 9, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 12, 'GLU:plan': 9, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 328 Chain: "F" Number of atoms: 1376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1376 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain: "G" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1169 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 142} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1063 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 124} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "I" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'ALO:plan-1': 1, 'G5G:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'ALO:plan-1': 1, 'G5G:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "O" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'ALO:plan-1': 1, 'G5G:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'ALO:plan-1': 1, 'G5G:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'ALO:plan-1': 1, 'G5G:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.40, per 1000 atoms: 0.53 Number of scatterers: 27396 At special positions: 0 Unit cell: (177.556, 143.154, 221.945, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 143 16.00 P 14 15.00 Mg 6 11.99 O 5230 8.00 N 4684 7.00 C 17319 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.11 Conformation dependent library (CDL) restraints added in 4.8 seconds 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6606 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 138 helices and 36 sheets defined 39.0% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.26 Creating SS restraints... Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 102 through 114 Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 160 through 166 Processing helix chain 'A' and resid 214 through 227 removed outlier: 4.000A pdb=" N ARG A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 285 through 288 No H-bonds generated for 'chain 'A' and resid 285 through 288' Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 307 through 317 Processing helix chain 'A' and resid 320 through 326 removed outlier: 5.584A pdb=" N LYS A 324 " --> pdb=" O ASP A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 342 through 365 Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 406 through 412 Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 182 through 196 Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 253 through 262 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 264 through 267 No H-bonds generated for 'chain 'B' and resid 264 through 267' Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 287 through 294 removed outlier: 3.974A pdb=" N LYS B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TYR B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 324 Processing helix chain 'B' and resid 346 through 361 removed outlier: 3.639A pdb=" N ALA B 349 " --> pdb=" O ARG B 346 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL B 350 " --> pdb=" O ARG B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 384 removed outlier: 3.691A pdb=" N ASP B 383 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 59 through 65 Processing helix chain 'D' and resid 68 through 74 Processing helix chain 'D' and resid 102 through 112 Processing helix chain 'D' and resid 114 through 118 Processing helix chain 'D' and resid 121 through 138 Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 187 through 203 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 248 through 250 No H-bonds generated for 'chain 'D' and resid 248 through 250' Processing helix chain 'D' and resid 255 through 298 removed outlier: 5.142A pdb=" N ARG D 266 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASN D 267 " --> pdb=" O GLN D 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 56 removed outlier: 5.108A pdb=" N PHE E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 83 removed outlier: 3.721A pdb=" N LEU E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 100 Processing helix chain 'E' and resid 127 through 148 Processing helix chain 'E' and resid 159 through 165 removed outlier: 4.301A pdb=" N SER E 165 " --> pdb=" O TRP E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 171 No H-bonds generated for 'chain 'E' and resid 169 through 171' Processing helix chain 'F' and resid 4 through 19 Processing helix chain 'F' and resid 37 through 40 No H-bonds generated for 'chain 'F' and resid 37 through 40' Processing helix chain 'F' and resid 81 through 96 Processing helix chain 'F' and resid 120 through 125 Processing helix chain 'F' and resid 129 through 167 removed outlier: 4.604A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 49 Proline residue: G 41 - end of helix Processing helix chain 'G' and resid 52 through 59 Processing helix chain 'G' and resid 71 through 85 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 101 through 115 Processing helix chain 'G' and resid 124 through 136 Processing helix chain 'G' and resid 139 through 146 Processing helix chain 'H' and resid 236 through 247 Processing helix chain 'H' and resid 253 through 265 Processing helix chain 'H' and resid 276 through 291 Processing helix chain 'H' and resid 300 through 309 Processing helix chain 'H' and resid 326 through 337 Processing helix chain 'H' and resid 345 through 358 Processing helix chain 'I' and resid 55 through 60 Processing helix chain 'I' and resid 79 through 91 Processing helix chain 'I' and resid 98 through 100 No H-bonds generated for 'chain 'I' and resid 98 through 100' Processing helix chain 'I' and resid 113 through 126 Processing helix chain 'I' and resid 139 through 145 Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 182 through 196 Processing helix chain 'I' and resid 203 through 215 Processing helix chain 'I' and resid 223 through 232 Processing helix chain 'I' and resid 252 through 256 Processing helix chain 'I' and resid 259 through 262 No H-bonds generated for 'chain 'I' and resid 259 through 262' Processing helix chain 'I' and resid 264 through 266 No H-bonds generated for 'chain 'I' and resid 264 through 266' Processing helix chain 'I' and resid 274 through 284 Processing helix chain 'I' and resid 287 through 295 removed outlier: 4.460A pdb=" N ASP I 292 " --> pdb=" O ASP I 288 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA I 295 " --> pdb=" O LYS I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 309 through 320 Processing helix chain 'I' and resid 338 through 348 Processing helix chain 'I' and resid 351 through 355 removed outlier: 3.897A pdb=" N MET I 355 " --> pdb=" O THR I 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 351 through 355' Processing helix chain 'I' and resid 359 through 365 Processing helix chain 'I' and resid 367 through 373 removed outlier: 4.113A pdb=" N LYS I 373 " --> pdb=" O VAL I 370 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'J' and resid 79 through 91 Processing helix chain 'J' and resid 98 through 100 No H-bonds generated for 'chain 'J' and resid 98 through 100' Processing helix chain 'J' and resid 113 through 125 Processing helix chain 'J' and resid 137 through 145 removed outlier: 3.779A pdb=" N SER J 145 " --> pdb=" O SER J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 196 Processing helix chain 'J' and resid 203 through 215 Processing helix chain 'J' and resid 223 through 232 Processing helix chain 'J' and resid 252 through 262 removed outlier: 4.340A pdb=" N CYS J 257 " --> pdb=" O ARG J 254 " (cutoff:3.500A) Proline residue: J 258 - end of helix Processing helix chain 'J' and resid 264 through 266 No H-bonds generated for 'chain 'J' and resid 264 through 266' Processing helix chain 'J' and resid 274 through 284 Processing helix chain 'J' and resid 287 through 295 removed outlier: 3.633A pdb=" N ALA J 295 " --> pdb=" O LYS J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 305 No H-bonds generated for 'chain 'J' and resid 303 through 305' Processing helix chain 'J' and resid 309 through 320 Processing helix chain 'J' and resid 335 through 348 removed outlier: 4.815A pdb=" N VAL J 339 " --> pdb=" O LYS J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 351 through 355 Processing helix chain 'J' and resid 359 through 365 Processing helix chain 'J' and resid 367 through 373 removed outlier: 3.534A pdb=" N LYS J 373 " --> pdb=" O VAL J 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 60 Processing helix chain 'K' and resid 79 through 91 Processing helix chain 'K' and resid 113 through 125 Processing helix chain 'K' and resid 137 through 145 Processing helix chain 'K' and resid 172 through 174 No H-bonds generated for 'chain 'K' and resid 172 through 174' Processing helix chain 'K' and resid 182 through 196 Processing helix chain 'K' and resid 203 through 216 Processing helix chain 'K' and resid 223 through 232 Processing helix chain 'K' and resid 253 through 262 Proline residue: K 258 - end of helix Processing helix chain 'K' and resid 264 through 266 No H-bonds generated for 'chain 'K' and resid 264 through 266' Processing helix chain 'K' and resid 274 through 283 Processing helix chain 'K' and resid 287 through 295 removed outlier: 4.393A pdb=" N LYS K 291 " --> pdb=" O ILE K 287 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ASP K 292 " --> pdb=" O ASP K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 303 through 305 No H-bonds generated for 'chain 'K' and resid 303 through 305' Processing helix chain 'K' and resid 309 through 320 Processing helix chain 'K' and resid 338 through 348 Processing helix chain 'K' and resid 351 through 355 removed outlier: 3.846A pdb=" N MET K 355 " --> pdb=" O THR K 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 351 through 355' Processing helix chain 'K' and resid 359 through 364 Processing helix chain 'K' and resid 367 through 373 removed outlier: 3.803A pdb=" N LYS K 373 " --> pdb=" O VAL K 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 79 through 91 Processing helix chain 'L' and resid 113 through 125 Processing helix chain 'L' and resid 137 through 145 Processing helix chain 'L' and resid 182 through 196 Processing helix chain 'L' and resid 203 through 216 Processing helix chain 'L' and resid 223 through 232 Processing helix chain 'L' and resid 253 through 262 Proline residue: L 258 - end of helix Processing helix chain 'L' and resid 264 through 267 No H-bonds generated for 'chain 'L' and resid 264 through 267' Processing helix chain 'L' and resid 274 through 283 Processing helix chain 'L' and resid 287 through 295 removed outlier: 4.430A pdb=" N ASP L 292 " --> pdb=" O ASP L 288 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA L 295 " --> pdb=" O LYS L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 309 through 320 Processing helix chain 'L' and resid 337 through 348 Processing helix chain 'L' and resid 352 through 355 Processing helix chain 'L' and resid 359 through 365 Processing helix chain 'L' and resid 367 through 371 Processing sheet with id= A, first strand: chain 'A' and resid 8 through 11 Processing sheet with id= B, first strand: chain 'A' and resid 126 through 129 Processing sheet with id= C, first strand: chain 'A' and resid 183 through 186 Processing sheet with id= D, first strand: chain 'A' and resid 267 through 269 Processing sheet with id= E, first strand: chain 'B' and resid 6 through 8 removed outlier: 4.074A pdb=" N VAL B 7 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY B 18 " --> pdb=" O VAL B 7 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.397A pdb=" N VAL B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N SER B 300 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= H, first strand: chain 'C' and resid 26 through 29 Processing sheet with id= I, first strand: chain 'C' and resid 39 through 41 Processing sheet with id= J, first strand: chain 'C' and resid 61 through 64 removed outlier: 3.738A pdb=" N ASN C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 135 through 141 removed outlier: 4.499A pdb=" N TRP C 135 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 170 through 173 Processing sheet with id= M, first strand: chain 'C' and resid 210 through 213 Processing sheet with id= N, first strand: chain 'C' and resid 264 through 267 removed outlier: 4.217A pdb=" N ALA C 267 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLN C 278 " --> pdb=" O HIS C 286 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N HIS C 286 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN C 280 " --> pdb=" O TRP C 284 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TRP C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 350 through 352 removed outlier: 3.783A pdb=" N HIS C 8 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU C 374 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL C 6 " --> pdb=" O LEU C 374 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N THR C 376 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N SER C 4 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 30 through 33 Processing sheet with id= Q, first strand: chain 'D' and resid 156 through 159 Processing sheet with id= R, first strand: chain 'F' and resid 51 through 53 Processing sheet with id= S, first strand: chain 'I' and resid 8 through 12 Processing sheet with id= T, first strand: chain 'I' and resid 35 through 38 Processing sheet with id= U, first strand: chain 'I' and resid 297 through 300 removed outlier: 6.501A pdb=" N ILE I 151 " --> pdb=" O VAL I 298 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER I 300 " --> pdb=" O ILE I 151 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU I 153 " --> pdb=" O SER I 300 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 238 through 240 Processing sheet with id= W, first strand: chain 'J' and resid 9 through 12 Processing sheet with id= X, first strand: chain 'J' and resid 52 through 54 Processing sheet with id= Y, first strand: chain 'J' and resid 297 through 299 removed outlier: 6.365A pdb=" N ILE J 151 " --> pdb=" O VAL J 298 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 238 through 241 Processing sheet with id= AA, first strand: chain 'K' and resid 8 through 11 Processing sheet with id= AB, first strand: chain 'K' and resid 35 through 38 Processing sheet with id= AC, first strand: chain 'K' and resid 105 through 107 removed outlier: 3.765A pdb=" N ALA K 135 " --> pdb=" O LEU K 105 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'K' and resid 297 through 300 removed outlier: 6.052A pdb=" N ILE K 151 " --> pdb=" O VAL K 298 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N SER K 300 " --> pdb=" O ILE K 151 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU K 153 " --> pdb=" O SER K 300 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'K' and resid 238 through 241 Processing sheet with id= AF, first strand: chain 'L' and resid 8 through 12 Processing sheet with id= AG, first strand: chain 'L' and resid 65 through 69 Processing sheet with id= AH, first strand: chain 'L' and resid 103 through 106 removed outlier: 3.982A pdb=" N TYR L 133 " --> pdb=" O THR L 103 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 297 through 300 removed outlier: 6.427A pdb=" N ILE L 151 " --> pdb=" O VAL L 298 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N SER L 300 " --> pdb=" O ILE L 151 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU L 153 " --> pdb=" O SER L 300 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 238 through 241 1080 hydrogen bonds defined for protein. 2856 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: 7.90 Time building geometry restraints manager: 11.88 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: 9009 1.34 - 1.46: 6185 1.46 - 1.58: 12521 1.58 - 1.70: 24 1.70 - 1.81: 239 Bond restraints: 27978 Sorted by residual: bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.63e+01 bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.53e+01 bond pdb=" C5 ATP A 501 " pdb=" C6 ATP A 501 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.25e+01 bond pdb=" C5 ATP B 501 " pdb=" C6 ATP B 501 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.23e+01 bond pdb=" C8 ATP A 501 " pdb=" N7 ATP A 501 " ideal model delta sigma weight residual 1.310 1.359 -0.049 1.00e-02 1.00e+04 2.37e+01 ... (remaining 27973 not shown) Histogram of bond angle deviations from ideal: 100.15 - 107.41: 1137 107.41 - 114.66: 16499 114.66 - 121.91: 14484 121.91 - 129.16: 5741 129.16 - 136.41: 175 Bond angle restraints: 38036 Sorted by residual: angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 120.07 19.80 1.00e+00 1.00e+00 3.92e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 120.16 19.71 1.00e+00 1.00e+00 3.89e+02 angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 120.26 16.57 1.00e+00 1.00e+00 2.75e+02 angle pdb=" PA ATP B 501 " pdb=" O3A ATP B 501 " pdb=" PB ATP B 501 " ideal model delta sigma weight residual 136.83 120.29 16.54 1.00e+00 1.00e+00 2.73e+02 angle pdb=" C5 ATP B 501 " pdb=" C4 ATP B 501 " pdb=" N3 ATP B 501 " ideal model delta sigma weight residual 126.80 118.74 8.06 1.00e+00 1.00e+00 6.49e+01 ... (remaining 38031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.89: 16200 25.89 - 51.78: 583 51.78 - 77.67: 77 77.67 - 103.55: 6 103.55 - 129.44: 1 Dihedral angle restraints: 16867 sinusoidal: 6632 harmonic: 10235 Sorted by residual: dihedral pdb=" O1B ADP L 401 " pdb=" O3A ADP L 401 " pdb=" PB ADP L 401 " pdb=" PA ADP L 401 " ideal model delta sinusoidal sigma weight residual 300.00 170.56 129.44 1 2.00e+01 2.50e-03 3.92e+01 dihedral pdb=" CA VAL L 30 " pdb=" C VAL L 30 " pdb=" N PHE L 31 " pdb=" CA PHE L 31 " ideal model delta harmonic sigma weight residual -180.00 -155.82 -24.18 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA VAL I 30 " pdb=" C VAL I 30 " pdb=" N PHE I 31 " pdb=" CA PHE I 31 " ideal model delta harmonic sigma weight residual -180.00 -158.61 -21.39 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 16864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3130 0.035 - 0.070: 712 0.070 - 0.105: 303 0.105 - 0.140: 133 0.140 - 0.175: 6 Chirality restraints: 4284 Sorted by residual: chirality pdb=" CB ALO P 6 " pdb=" CA ALO P 6 " pdb=" OG1 ALO P 6 " pdb=" CG2 ALO P 6 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CB ALO Q 6 " pdb=" CA ALO Q 6 " pdb=" OG1 ALO Q 6 " pdb=" CG2 ALO Q 6 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 7.60e-01 chirality pdb=" CB ALO O 6 " pdb=" CA ALO O 6 " pdb=" OG1 ALO O 6 " pdb=" CG2 ALO O 6 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 7.52e-01 ... (remaining 4281 not shown) Planarity restraints: 4891 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 5 " 0.017 2.00e-02 2.50e+03 3.53e-02 1.24e+01 pdb=" C GLN C 5 " -0.061 2.00e-02 2.50e+03 pdb=" O GLN C 5 " 0.023 2.00e-02 2.50e+03 pdb=" N VAL C 6 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE H 293 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO H 294 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO H 294 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 294 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 257 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO B 258 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 258 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 258 " 0.019 5.00e-02 4.00e+02 ... (remaining 4888 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 172 2.50 - 3.10: 21847 3.10 - 3.70: 41401 3.70 - 4.30: 58407 4.30 - 4.90: 95577 Nonbonded interactions: 217404 Sorted by model distance: nonbonded pdb=" O LEU A 19 " pdb=" O SER A 28 " model vdw 1.894 3.040 nonbonded pdb=" O3B ADP I 401 " pdb="MG MG I 402 " model vdw 1.974 2.170 nonbonded pdb=" O1B ADP L 401 " pdb="MG MG L 402 " model vdw 1.974 2.170 nonbonded pdb=" O3B ADP J 401 " pdb="MG MG J 402 " model vdw 1.974 2.170 nonbonded pdb=" O3B ADP K 401 " pdb="MG MG K 402 " model vdw 1.975 2.170 ... (remaining 217399 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 'I' and (resid 5 through 374 or resid 401 through 402)) selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.120 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 69.870 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.200 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 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 : 0.003 0.081 27978 Z= 0.195 Angle : 0.586 19.797 38036 Z= 0.351 Chirality : 0.040 0.175 4284 Planarity : 0.003 0.039 4891 Dihedral : 13.380 129.442 10261 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.13), residues: 3433 helix: -0.64 (0.13), residues: 1436 sheet: -2.99 (0.18), residues: 590 loop : -3.20 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 375 HIS 0.004 0.000 HIS D 261 PHE 0.009 0.001 PHE C 115 TYR 0.009 0.000 TYR A 29 ARG 0.006 0.000 ARG H 318 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 589 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.8972 (mtt90) cc_final: 0.8657 (mtt90) REVERT: B 154 ASP cc_start: 0.8172 (t0) cc_final: 0.7811 (t0) REVERT: B 172 ASN cc_start: 0.8256 (t0) cc_final: 0.7840 (t0) REVERT: B 342 ASP cc_start: 0.8435 (t0) cc_final: 0.7978 (t0) REVERT: C 62 ASP cc_start: 0.8614 (t0) cc_final: 0.8262 (t0) REVERT: C 169 LYS cc_start: 0.9241 (mttt) cc_final: 0.9009 (mttm) REVERT: C 227 SER cc_start: 0.9118 (m) cc_final: 0.8879 (p) REVERT: C 245 ILE cc_start: 0.9301 (mt) cc_final: 0.9058 (tt) REVERT: D 1 MET cc_start: 0.6488 (ptm) cc_final: 0.5534 (ptm) REVERT: F 61 CYS cc_start: 0.7922 (m) cc_final: 0.7606 (m) REVERT: F 64 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7809 (mm-30) REVERT: F 133 ASP cc_start: 0.8799 (m-30) cc_final: 0.8241 (m-30) REVERT: G 131 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8338 (tm-30) REVERT: G 132 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8761 (mmmm) REVERT: H 249 LYS cc_start: 0.8000 (tppt) cc_final: 0.7579 (tppt) REVERT: J 313 MET cc_start: 0.8192 (tpt) cc_final: 0.7839 (tpt) REVERT: J 328 LYS cc_start: 0.8805 (tttt) cc_final: 0.8594 (ttpp) REVERT: K 81 ASP cc_start: 0.8782 (m-30) cc_final: 0.8553 (m-30) REVERT: K 83 GLU cc_start: 0.8849 (tt0) cc_final: 0.8495 (tt0) REVERT: K 103 THR cc_start: 0.9267 (t) cc_final: 0.8912 (p) REVERT: K 118 LYS cc_start: 0.8863 (tppp) cc_final: 0.8585 (mmtt) REVERT: K 169 TYR cc_start: 0.7663 (m-80) cc_final: 0.7149 (t80) REVERT: K 217 CYS cc_start: 0.8531 (m) cc_final: 0.7621 (m) REVERT: L 78 ASN cc_start: 0.7420 (t0) cc_final: 0.6693 (t0) REVERT: L 81 ASP cc_start: 0.8569 (m-30) cc_final: 0.8293 (m-30) REVERT: L 92 ASN cc_start: 0.8452 (m-40) cc_final: 0.8056 (m110) REVERT: L 165 ILE cc_start: 0.8694 (mm) cc_final: 0.8493 (tp) REVERT: L 214 GLU cc_start: 0.7340 (pt0) cc_final: 0.7077 (pt0) REVERT: L 263 GLN cc_start: 0.7418 (mm-40) cc_final: 0.7145 (mt0) REVERT: L 265 SER cc_start: 0.8327 (p) cc_final: 0.8045 (t) REVERT: L 276 GLU cc_start: 0.8547 (tt0) cc_final: 0.8194 (tt0) REVERT: L 305 MET cc_start: 0.8159 (tpt) cc_final: 0.7917 (mmt) REVERT: L 313 MET cc_start: 0.6765 (tpt) cc_final: 0.6311 (tpt) REVERT: L 334 GLU cc_start: 0.7720 (pm20) cc_final: 0.7490 (pm20) outliers start: 0 outliers final: 0 residues processed: 589 average time/residue: 0.4274 time to fit residues: 387.6526 Evaluate side-chains 382 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 292 optimal weight: 6.9990 chunk 262 optimal weight: 3.9990 chunk 145 optimal weight: 30.0000 chunk 89 optimal weight: 3.9990 chunk 176 optimal weight: 8.9990 chunk 140 optimal weight: 50.0000 chunk 271 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 201 optimal weight: 7.9990 chunk 314 optimal weight: 9.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 134 ASN A 151 ASN A 192 HIS B 227 HIS C 343 HIS ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN H 277 ASN I 59 GLN ** I 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 161 HIS K 354 GLN L 88 HIS L 92 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 27978 Z= 0.420 Angle : 0.740 8.978 38036 Z= 0.373 Chirality : 0.049 0.205 4284 Planarity : 0.005 0.049 4891 Dihedral : 8.511 106.276 4016 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.15 % Allowed : 10.39 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.14), residues: 3433 helix: 0.08 (0.14), residues: 1429 sheet: -2.29 (0.19), residues: 583 loop : -2.38 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 387 HIS 0.008 0.002 HIS D 249 PHE 0.033 0.002 PHE I 262 TYR 0.025 0.002 TYR D 279 ARG 0.010 0.001 ARG K 254 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 410 time to evaluate : 3.482 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: A 29 TYR cc_start: 0.7237 (m-80) cc_final: 0.7032 (m-10) REVERT: A 146 MET cc_start: 0.8654 (tpp) cc_final: 0.8073 (tpp) REVERT: A 160 GLN cc_start: 0.8356 (mt0) cc_final: 0.8023 (mp10) REVERT: B 145 GLN cc_start: 0.8780 (tp40) cc_final: 0.8545 (tp40) REVERT: B 172 ASN cc_start: 0.8751 (t0) cc_final: 0.8416 (t0) REVERT: B 212 MET cc_start: 0.8368 (ttm) cc_final: 0.7998 (ttp) REVERT: B 270 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7305 (mp0) REVERT: C 37 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8873 (tp) REVERT: C 153 ASP cc_start: 0.8868 (t0) cc_final: 0.8512 (t0) REVERT: C 169 LYS cc_start: 0.9388 (mttt) cc_final: 0.9139 (mttm) REVERT: C 245 ILE cc_start: 0.9316 (mt) cc_final: 0.9054 (tt) REVERT: D 59 TYR cc_start: 0.9143 (t80) cc_final: 0.8896 (t80) REVERT: D 109 MET cc_start: 0.9144 (tpt) cc_final: 0.8931 (tpt) REVERT: F 1 MET cc_start: 0.5960 (tmm) cc_final: 0.4800 (tmm) REVERT: F 64 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7808 (mp0) REVERT: F 89 LYS cc_start: 0.8670 (tptp) cc_final: 0.7872 (tppp) REVERT: F 92 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8607 (tm-30) REVERT: F 137 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8518 (mm-30) REVERT: G 113 ARG cc_start: 0.8763 (tpp-160) cc_final: 0.8537 (mmt90) REVERT: G 151 ASP cc_start: 0.8571 (p0) cc_final: 0.8152 (p0) REVERT: H 349 ARG cc_start: 0.8824 (ttp80) cc_final: 0.8190 (ptm160) REVERT: I 68 LYS cc_start: 0.8574 (mttt) cc_final: 0.8314 (mtmm) REVERT: I 83 GLU cc_start: 0.8503 (pp20) cc_final: 0.8271 (pp20) REVERT: I 184 ASP cc_start: 0.8537 (m-30) cc_final: 0.8328 (m-30) REVERT: I 286 ASP cc_start: 0.7480 (m-30) cc_final: 0.7276 (m-30) REVERT: J 132 MET cc_start: 0.8747 (ppp) cc_final: 0.8186 (ppp) REVERT: J 288 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7895 (p0) REVERT: K 81 ASP cc_start: 0.8985 (m-30) cc_final: 0.8702 (m-30) REVERT: K 103 THR cc_start: 0.9440 (t) cc_final: 0.9096 (p) REVERT: K 123 MET cc_start: 0.8692 (tpp) cc_final: 0.8355 (tpp) REVERT: K 136 ILE cc_start: 0.9197 (mm) cc_final: 0.8841 (mm) REVERT: K 169 TYR cc_start: 0.8038 (m-80) cc_final: 0.7266 (t80) REVERT: K 217 CYS cc_start: 0.8775 (m) cc_final: 0.8277 (m) REVERT: K 283 MET cc_start: 0.8928 (mmm) cc_final: 0.8615 (mmm) REVERT: L 82 MET cc_start: 0.9013 (mmm) cc_final: 0.8592 (tmm) REVERT: L 92 ASN cc_start: 0.8503 (m110) cc_final: 0.8114 (m-40) REVERT: L 99 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8398 (mt-10) REVERT: L 157 ASP cc_start: 0.6820 (t0) cc_final: 0.6614 (t0) REVERT: L 165 ILE cc_start: 0.8864 (mm) cc_final: 0.8639 (tp) REVERT: L 210 ARG cc_start: 0.8447 (tmm-80) cc_final: 0.8073 (ttp80) REVERT: L 263 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7349 (mt0) REVERT: L 265 SER cc_start: 0.8687 (p) cc_final: 0.8463 (t) REVERT: L 334 GLU cc_start: 0.7832 (pm20) cc_final: 0.7621 (pm20) outliers start: 61 outliers final: 38 residues processed: 443 average time/residue: 0.3806 time to fit residues: 271.2043 Evaluate side-chains 392 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 352 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 286 PHE Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain H residue 334 ASN Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 305 MET Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 288 ASP Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 227 MET Chi-restraints excluded: chain L residue 12 ASN Chi-restraints excluded: chain L residue 115 ASN Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain L residue 217 CYS Chi-restraints excluded: chain L residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 174 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 314 optimal weight: 8.9990 chunk 340 optimal weight: 0.0470 chunk 280 optimal weight: 0.7980 chunk 312 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 252 optimal weight: 0.9980 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 GLN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 363 GLN C 196 ASN C 343 HIS D 8 ASN D 261 HIS D 272 HIS ** F 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 GLN I 59 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27978 Z= 0.182 Angle : 0.584 8.682 38036 Z= 0.287 Chirality : 0.043 0.228 4284 Planarity : 0.004 0.052 4891 Dihedral : 8.319 103.272 4016 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.36 % Allowed : 13.50 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.15), residues: 3433 helix: 0.45 (0.14), residues: 1430 sheet: -1.85 (0.20), residues: 579 loop : -1.99 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 387 HIS 0.006 0.001 HIS H 339 PHE 0.017 0.001 PHE I 262 TYR 0.016 0.001 TYR D 279 ARG 0.005 0.000 ARG K 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 374 time to evaluate : 3.033 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: A 29 TYR cc_start: 0.7159 (m-80) cc_final: 0.6909 (m-80) REVERT: A 160 GLN cc_start: 0.8338 (mt0) cc_final: 0.7942 (mp10) REVERT: A 239 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8674 (mtt90) REVERT: B 145 GLN cc_start: 0.8762 (tp40) cc_final: 0.8498 (tp40) REVERT: B 212 MET cc_start: 0.8360 (ttm) cc_final: 0.8106 (ttp) REVERT: C 62 ASP cc_start: 0.8803 (t0) cc_final: 0.8435 (t0) REVERT: C 153 ASP cc_start: 0.8788 (t0) cc_final: 0.8445 (t0) REVERT: C 169 LYS cc_start: 0.9339 (mttt) cc_final: 0.9132 (mttm) REVERT: C 196 ASN cc_start: 0.9450 (OUTLIER) cc_final: 0.9162 (t0) REVERT: D 157 MET cc_start: 0.6572 (tpp) cc_final: 0.6224 (tpt) REVERT: F 89 LYS cc_start: 0.8641 (tptp) cc_final: 0.8058 (tppp) REVERT: F 92 GLN cc_start: 0.9036 (tm-30) cc_final: 0.8595 (tm-30) REVERT: F 137 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8461 (mm-30) REVERT: G 18 GLU cc_start: 0.8414 (mp0) cc_final: 0.8195 (mp0) REVERT: G 27 GLU cc_start: 0.6538 (mm-30) cc_final: 0.6168 (tp30) REVERT: G 131 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8523 (tm-30) REVERT: G 151 ASP cc_start: 0.8431 (p0) cc_final: 0.7957 (p0) REVERT: H 243 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8280 (m-80) REVERT: H 349 ARG cc_start: 0.8793 (ttp80) cc_final: 0.8196 (ptm-80) REVERT: I 68 LYS cc_start: 0.8559 (mttt) cc_final: 0.8334 (mtmm) REVERT: I 325 MET cc_start: 0.8590 (tpp) cc_final: 0.7795 (mpp) REVERT: J 82 MET cc_start: 0.9254 (tpp) cc_final: 0.8916 (mmm) REVERT: J 123 MET cc_start: 0.8870 (tpp) cc_final: 0.8650 (tpp) REVERT: J 132 MET cc_start: 0.8684 (ppp) cc_final: 0.8172 (ppp) REVERT: K 103 THR cc_start: 0.9376 (t) cc_final: 0.9073 (p) REVERT: K 123 MET cc_start: 0.8648 (tpp) cc_final: 0.8264 (tpp) REVERT: K 136 ILE cc_start: 0.9147 (mm) cc_final: 0.8909 (mt) REVERT: K 169 TYR cc_start: 0.7862 (m-80) cc_final: 0.7232 (t80) REVERT: K 217 CYS cc_start: 0.8726 (m) cc_final: 0.8147 (m) REVERT: K 283 MET cc_start: 0.8936 (mmm) cc_final: 0.8615 (mmm) REVERT: K 316 GLU cc_start: 0.8852 (tp30) cc_final: 0.8588 (tp30) REVERT: L 92 ASN cc_start: 0.8442 (m110) cc_final: 0.8106 (m-40) REVERT: L 99 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8404 (mt-10) REVERT: L 165 ILE cc_start: 0.8748 (mm) cc_final: 0.8536 (tp) REVERT: L 210 ARG cc_start: 0.8395 (tmm-80) cc_final: 0.8069 (ttp80) REVERT: L 263 GLN cc_start: 0.7642 (mm-40) cc_final: 0.7238 (mt0) REVERT: L 265 SER cc_start: 0.8664 (p) cc_final: 0.8415 (t) REVERT: L 334 GLU cc_start: 0.7658 (pm20) cc_final: 0.7415 (pm20) REVERT: L 360 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7781 (tm-30) outliers start: 67 outliers final: 45 residues processed: 415 average time/residue: 0.3724 time to fit residues: 247.6381 Evaluate side-chains 391 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 343 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 70 GLN Chi-restraints excluded: chain H residue 243 PHE Chi-restraints excluded: chain H residue 286 PHE Chi-restraints excluded: chain H residue 288 ARG Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 305 MET Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain J residue 267 ILE Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 227 MET Chi-restraints excluded: chain L residue 12 ASN Chi-restraints excluded: chain L residue 132 MET Chi-restraints excluded: chain L residue 173 HIS Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 310 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 315 optimal weight: 0.8980 chunk 334 optimal weight: 0.8980 chunk 165 optimal weight: 0.3980 chunk 299 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS C 133 ASN C 343 HIS ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 263 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 27978 Z= 0.263 Angle : 0.604 8.888 38036 Z= 0.298 Chirality : 0.044 0.215 4284 Planarity : 0.004 0.056 4891 Dihedral : 8.237 101.621 4016 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.10 % Allowed : 14.59 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.15), residues: 3433 helix: 0.51 (0.14), residues: 1424 sheet: -1.62 (0.20), residues: 588 loop : -1.83 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 86 HIS 0.009 0.001 HIS H 339 PHE 0.015 0.001 PHE I 255 TYR 0.017 0.001 TYR C 202 ARG 0.005 0.000 ARG D 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 362 time to evaluate : 3.263 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: A 160 GLN cc_start: 0.8485 (mt0) cc_final: 0.8003 (mp10) REVERT: A 239 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.8677 (mtt90) REVERT: B 113 VAL cc_start: 0.9178 (m) cc_final: 0.8898 (p) REVERT: B 127 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7590 (m-80) REVERT: B 212 MET cc_start: 0.8475 (ttm) cc_final: 0.8202 (ttp) REVERT: C 62 ASP cc_start: 0.8820 (t0) cc_final: 0.8456 (t0) REVERT: C 153 ASP cc_start: 0.8838 (t0) cc_final: 0.8473 (t0) REVERT: C 169 LYS cc_start: 0.9391 (mttt) cc_final: 0.9149 (mttm) REVERT: C 286 HIS cc_start: 0.9098 (OUTLIER) cc_final: 0.7976 (p-80) REVERT: D 8 ASN cc_start: 0.9068 (t0) cc_final: 0.8828 (m-40) REVERT: F 89 LYS cc_start: 0.8894 (tptp) cc_final: 0.8292 (tppp) REVERT: F 92 GLN cc_start: 0.9082 (tm-30) cc_final: 0.8655 (tm-30) REVERT: F 137 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8475 (mm-30) REVERT: G 119 GLN cc_start: 0.8573 (pm20) cc_final: 0.8366 (pm20) REVERT: G 151 ASP cc_start: 0.8530 (p0) cc_final: 0.8016 (p0) REVERT: H 243 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8367 (m-80) REVERT: H 349 ARG cc_start: 0.8785 (ttp80) cc_final: 0.8058 (ptm160) REVERT: I 68 LYS cc_start: 0.8566 (mttt) cc_final: 0.8332 (mtmm) REVERT: I 283 MET cc_start: 0.9138 (mmp) cc_final: 0.8604 (mmp) REVERT: I 325 MET cc_start: 0.8625 (tpp) cc_final: 0.7897 (mpp) REVERT: J 75 ILE cc_start: 0.8830 (mp) cc_final: 0.8138 (tt) REVERT: J 82 MET cc_start: 0.9302 (tpp) cc_final: 0.8899 (mmm) REVERT: J 132 MET cc_start: 0.8688 (ppp) cc_final: 0.8190 (ppp) REVERT: J 316 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7202 (tt0) REVERT: K 103 THR cc_start: 0.9379 (t) cc_final: 0.9161 (p) REVERT: K 123 MET cc_start: 0.8690 (tpp) cc_final: 0.8374 (tpp) REVERT: K 169 TYR cc_start: 0.7920 (m-80) cc_final: 0.7195 (t80) REVERT: K 217 CYS cc_start: 0.8738 (m) cc_final: 0.8181 (m) REVERT: L 92 ASN cc_start: 0.8388 (m110) cc_final: 0.8026 (m-40) REVERT: L 165 ILE cc_start: 0.8833 (mm) cc_final: 0.8596 (tp) REVERT: L 214 GLU cc_start: 0.7560 (pt0) cc_final: 0.7264 (pt0) REVERT: L 263 GLN cc_start: 0.7663 (mm-40) cc_final: 0.7185 (mt0) REVERT: L 265 SER cc_start: 0.8755 (p) cc_final: 0.8485 (t) REVERT: L 334 GLU cc_start: 0.7689 (pm20) cc_final: 0.7438 (pm20) REVERT: L 360 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7719 (tm-30) outliers start: 88 outliers final: 62 residues processed: 419 average time/residue: 0.3608 time to fit residues: 246.5319 Evaluate side-chains 401 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 334 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 243 PHE Chi-restraints excluded: chain H residue 286 PHE Chi-restraints excluded: chain H residue 288 ARG Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 334 ASN Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 305 MET Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain J residue 267 ILE Chi-restraints excluded: chain J residue 288 ASP Chi-restraints excluded: chain J residue 299 MET Chi-restraints excluded: chain J residue 316 GLU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 227 MET Chi-restraints excluded: chain L residue 12 ASN Chi-restraints excluded: chain L residue 132 MET Chi-restraints excluded: chain L residue 173 HIS Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain L residue 217 CYS Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain L residue 292 ASP Chi-restraints excluded: chain L residue 351 THR Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 278 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 249 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 285 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 300 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 GLN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 GLN K 40 HIS K 92 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27978 Z= 0.230 Angle : 0.593 8.873 38036 Z= 0.291 Chirality : 0.043 0.198 4284 Planarity : 0.004 0.058 4891 Dihedral : 8.104 97.606 4016 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.45 % Allowed : 15.50 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.15), residues: 3433 helix: 0.59 (0.14), residues: 1421 sheet: -1.45 (0.21), residues: 580 loop : -1.67 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 170 HIS 0.009 0.001 HIS H 339 PHE 0.015 0.001 PHE F 93 TYR 0.014 0.001 TYR F 8 ARG 0.004 0.000 ARG D 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 358 time to evaluate : 3.064 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: A 160 GLN cc_start: 0.8553 (mt0) cc_final: 0.7965 (mp-120) REVERT: A 239 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8924 (mmt-90) REVERT: B 113 VAL cc_start: 0.9174 (m) cc_final: 0.8887 (p) REVERT: B 127 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.7427 (m-80) REVERT: B 212 MET cc_start: 0.8470 (ttm) cc_final: 0.8195 (ttp) REVERT: C 62 ASP cc_start: 0.8818 (t0) cc_final: 0.8462 (t0) REVERT: C 66 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8679 (mppt) REVERT: C 153 ASP cc_start: 0.8840 (t0) cc_final: 0.8470 (t0) REVERT: C 169 LYS cc_start: 0.9405 (mttt) cc_final: 0.9162 (mttm) REVERT: C 286 HIS cc_start: 0.9170 (OUTLIER) cc_final: 0.8109 (p-80) REVERT: F 89 LYS cc_start: 0.8999 (tptp) cc_final: 0.8401 (tppp) REVERT: F 92 GLN cc_start: 0.9117 (tm-30) cc_final: 0.8686 (tm-30) REVERT: F 137 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8492 (mm-30) REVERT: G 27 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6613 (tp30) REVERT: G 119 GLN cc_start: 0.8549 (pm20) cc_final: 0.8323 (pm20) REVERT: G 151 ASP cc_start: 0.8549 (p0) cc_final: 0.8058 (p0) REVERT: H 243 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8403 (m-80) REVERT: H 248 GLU cc_start: 0.7088 (tp30) cc_final: 0.6731 (tp30) REVERT: H 349 ARG cc_start: 0.8870 (ttp80) cc_final: 0.8163 (ptm-80) REVERT: I 68 LYS cc_start: 0.8582 (mttt) cc_final: 0.8342 (mtmm) REVERT: J 82 MET cc_start: 0.9297 (tpp) cc_final: 0.8909 (mmm) REVERT: J 132 MET cc_start: 0.8671 (ppp) cc_final: 0.8186 (ppp) REVERT: J 261 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9081 (tt) REVERT: J 316 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7302 (tt0) REVERT: K 169 TYR cc_start: 0.7874 (m-80) cc_final: 0.7160 (t80) REVERT: K 217 CYS cc_start: 0.8739 (m) cc_final: 0.8067 (m) REVERT: L 92 ASN cc_start: 0.8374 (m110) cc_final: 0.8014 (m-40) REVERT: L 165 ILE cc_start: 0.8824 (mm) cc_final: 0.8581 (tp) REVERT: L 210 ARG cc_start: 0.8411 (tmm-80) cc_final: 0.8149 (ttp80) REVERT: L 263 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7080 (mt0) REVERT: L 265 SER cc_start: 0.8778 (p) cc_final: 0.8489 (t) REVERT: L 283 MET cc_start: 0.6867 (mmp) cc_final: 0.5225 (tmm) REVERT: L 360 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7714 (tm-30) outliers start: 98 outliers final: 68 residues processed: 428 average time/residue: 0.3646 time to fit residues: 254.4538 Evaluate side-chains 409 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 334 time to evaluate : 3.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 353 TYR Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 243 PHE Chi-restraints excluded: chain H residue 286 PHE Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 277 THR Chi-restraints excluded: chain I residue 305 MET Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 267 ILE Chi-restraints excluded: chain J residue 288 ASP Chi-restraints excluded: chain J residue 299 MET Chi-restraints excluded: chain J residue 316 GLU Chi-restraints excluded: chain J residue 340 TRP Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 227 MET Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain L residue 12 ASN Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 173 HIS Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 292 ASP Chi-restraints excluded: chain L residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 112 optimal weight: 9.9990 chunk 301 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 196 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 334 optimal weight: 7.9990 chunk 277 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 chunk 27 optimal weight: 0.0470 chunk 110 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 GLN J 115 ASN K 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 27978 Z= 0.420 Angle : 0.693 10.100 38036 Z= 0.346 Chirality : 0.047 0.212 4284 Planarity : 0.005 0.057 4891 Dihedral : 8.281 96.380 4016 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 4.58 % Allowed : 15.64 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.15), residues: 3433 helix: 0.58 (0.14), residues: 1383 sheet: -1.46 (0.20), residues: 602 loop : -1.66 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 86 HIS 0.010 0.001 HIS H 339 PHE 0.021 0.002 PHE J 255 TYR 0.016 0.002 TYR I 218 ARG 0.005 0.001 ARG D 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 349 time to evaluate : 3.484 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: A 239 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.8993 (mmt-90) REVERT: B 28 GLN cc_start: 0.9045 (pp30) cc_final: 0.8471 (pp30) REVERT: B 113 VAL cc_start: 0.9280 (m) cc_final: 0.9051 (p) REVERT: B 127 TYR cc_start: 0.8843 (OUTLIER) cc_final: 0.7738 (m-80) REVERT: C 62 ASP cc_start: 0.8856 (t0) cc_final: 0.8412 (t0) REVERT: C 66 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8725 (mppt) REVERT: C 153 ASP cc_start: 0.8872 (t0) cc_final: 0.8498 (t0) REVERT: C 169 LYS cc_start: 0.9406 (mttt) cc_final: 0.9199 (mttm) REVERT: C 286 HIS cc_start: 0.9320 (OUTLIER) cc_final: 0.8137 (p-80) REVERT: C 346 MET cc_start: 0.8687 (ttt) cc_final: 0.8435 (ttt) REVERT: D 109 MET cc_start: 0.9134 (tpt) cc_final: 0.8841 (tpp) REVERT: D 157 MET cc_start: 0.6880 (tpp) cc_final: 0.6392 (tpp) REVERT: D 264 VAL cc_start: 0.8120 (m) cc_final: 0.7847 (p) REVERT: D 284 MET cc_start: 0.8500 (mmt) cc_final: 0.8283 (mmt) REVERT: F 89 LYS cc_start: 0.8916 (tptp) cc_final: 0.8347 (tppp) REVERT: F 92 GLN cc_start: 0.9147 (tm-30) cc_final: 0.8696 (tm-30) REVERT: F 137 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8596 (mm-30) REVERT: G 27 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6895 (tp30) REVERT: G 84 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9089 (tt) REVERT: G 151 ASP cc_start: 0.8588 (p0) cc_final: 0.8237 (p0) REVERT: H 243 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8510 (m-80) REVERT: H 248 GLU cc_start: 0.7337 (tp30) cc_final: 0.6937 (tp30) REVERT: H 249 LYS cc_start: 0.7925 (tppt) cc_final: 0.7564 (tppt) REVERT: I 68 LYS cc_start: 0.8572 (mttt) cc_final: 0.8325 (mtmm) REVERT: J 261 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9126 (tt) REVERT: J 288 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7881 (p0) REVERT: J 325 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8268 (tpt) REVERT: K 16 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9088 (pp) REVERT: K 162 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8186 (p0) REVERT: K 169 TYR cc_start: 0.8016 (m-80) cc_final: 0.7122 (t80) REVERT: K 217 CYS cc_start: 0.8768 (m) cc_final: 0.8242 (m) REVERT: K 316 GLU cc_start: 0.9018 (tp30) cc_final: 0.8733 (tp30) REVERT: L 86 TRP cc_start: 0.8881 (m-10) cc_final: 0.8671 (m-10) REVERT: L 92 ASN cc_start: 0.8439 (m110) cc_final: 0.8072 (m-40) REVERT: L 157 ASP cc_start: 0.7058 (t0) cc_final: 0.6846 (t0) REVERT: L 165 ILE cc_start: 0.8832 (mm) cc_final: 0.8574 (tp) REVERT: L 214 GLU cc_start: 0.7622 (pt0) cc_final: 0.7344 (pt0) REVERT: L 263 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7210 (mt0) REVERT: L 360 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7759 (tm-30) outliers start: 130 outliers final: 85 residues processed: 441 average time/residue: 0.3803 time to fit residues: 277.3674 Evaluate side-chains 426 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 330 time to evaluate : 3.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 73 CYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 353 TYR Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 243 PHE Chi-restraints excluded: chain H residue 286 PHE Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain H residue 319 HIS Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 277 THR Chi-restraints excluded: chain I residue 305 MET Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 267 ILE Chi-restraints excluded: chain J residue 288 ASP Chi-restraints excluded: chain J residue 325 MET Chi-restraints excluded: chain J residue 340 TRP Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 227 MET Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain L residue 12 ASN Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 173 HIS Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain L residue 217 CYS Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 292 ASP Chi-restraints excluded: chain L residue 351 THR Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 322 optimal weight: 0.6980 chunk 37 optimal weight: 9.9990 chunk 190 optimal weight: 0.7980 chunk 244 optimal weight: 0.0770 chunk 189 optimal weight: 0.7980 chunk 281 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 333 optimal weight: 5.9990 chunk 208 optimal weight: 0.9990 chunk 203 optimal weight: 0.9990 chunk 153 optimal weight: 0.4980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN D 29 GLN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 GLN ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 ASN I 137 GLN J 115 ASN J 121 GLN K 92 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27978 Z= 0.162 Angle : 0.611 13.080 38036 Z= 0.293 Chirality : 0.043 0.189 4284 Planarity : 0.004 0.060 4891 Dihedral : 7.872 89.182 4016 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.89 % Allowed : 18.18 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 3433 helix: 0.73 (0.15), residues: 1401 sheet: -1.22 (0.21), residues: 586 loop : -1.55 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 170 HIS 0.007 0.001 HIS H 339 PHE 0.017 0.001 PHE F 93 TYR 0.015 0.001 TYR F 8 ARG 0.005 0.000 ARG D 287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 367 time to evaluate : 3.258 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: A 239 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.8964 (mmt-90) REVERT: B 28 GLN cc_start: 0.9003 (pp30) cc_final: 0.8423 (pp30) REVERT: B 113 VAL cc_start: 0.9097 (m) cc_final: 0.8837 (p) REVERT: B 127 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.7399 (m-80) REVERT: C 62 ASP cc_start: 0.8726 (t0) cc_final: 0.8423 (t0) REVERT: C 66 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8566 (mppt) REVERT: C 153 ASP cc_start: 0.8790 (t0) cc_final: 0.8416 (t0) REVERT: C 169 LYS cc_start: 0.9405 (mttt) cc_final: 0.9186 (mttm) REVERT: C 226 ASP cc_start: 0.8561 (t0) cc_final: 0.8209 (t0) REVERT: C 286 HIS cc_start: 0.9234 (OUTLIER) cc_final: 0.8106 (p-80) REVERT: F 89 LYS cc_start: 0.8860 (tptp) cc_final: 0.8261 (tppp) REVERT: F 92 GLN cc_start: 0.9133 (tm-30) cc_final: 0.8689 (tm-30) REVERT: F 137 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8538 (mm-30) REVERT: G 27 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6714 (tp30) REVERT: G 151 ASP cc_start: 0.8523 (p0) cc_final: 0.8091 (p0) REVERT: H 243 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8460 (m-80) REVERT: H 248 GLU cc_start: 0.7391 (tp30) cc_final: 0.7018 (tp30) REVERT: H 249 LYS cc_start: 0.7965 (tppt) cc_final: 0.7571 (tppt) REVERT: H 260 GLN cc_start: 0.8539 (mm-40) cc_final: 0.8302 (mm-40) REVERT: I 68 LYS cc_start: 0.8566 (mttt) cc_final: 0.8326 (mtmm) REVERT: I 107 GLU cc_start: 0.8109 (tt0) cc_final: 0.7860 (pt0) REVERT: I 113 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8511 (mmtt) REVERT: I 123 MET cc_start: 0.8387 (ttm) cc_final: 0.8089 (ttm) REVERT: I 283 MET cc_start: 0.9186 (mmp) cc_final: 0.8631 (mmp) REVERT: J 82 MET cc_start: 0.9282 (tpp) cc_final: 0.8867 (mmm) REVERT: J 123 MET cc_start: 0.8752 (tpp) cc_final: 0.8446 (ttm) REVERT: J 132 MET cc_start: 0.8826 (ppp) cc_final: 0.8497 (ppp) REVERT: J 261 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9083 (tt) REVERT: J 325 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8198 (mmm) REVERT: K 162 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8003 (p0) REVERT: K 169 TYR cc_start: 0.7781 (m-80) cc_final: 0.7121 (t80) REVERT: K 217 CYS cc_start: 0.8715 (m) cc_final: 0.7957 (m) REVERT: K 316 GLU cc_start: 0.8955 (tp30) cc_final: 0.8688 (tp30) REVERT: L 59 GLN cc_start: 0.8802 (tp40) cc_final: 0.8466 (tp40) REVERT: L 86 TRP cc_start: 0.8766 (m-10) cc_final: 0.8522 (m-10) REVERT: L 92 ASN cc_start: 0.8378 (m110) cc_final: 0.8041 (m-40) REVERT: L 165 ILE cc_start: 0.8803 (mm) cc_final: 0.8549 (tp) REVERT: L 210 ARG cc_start: 0.8394 (tmm-80) cc_final: 0.8154 (ttp80) REVERT: L 263 GLN cc_start: 0.7489 (mm-40) cc_final: 0.6781 (mt0) REVERT: L 283 MET cc_start: 0.6855 (mmp) cc_final: 0.5256 (tmm) REVERT: L 360 GLN cc_start: 0.8139 (tm-30) cc_final: 0.7834 (tm-30) outliers start: 82 outliers final: 54 residues processed: 421 average time/residue: 0.3611 time to fit residues: 247.2871 Evaluate side-chains 399 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 337 time to evaluate : 3.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 353 TYR Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain H residue 243 PHE Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 286 PHE Chi-restraints excluded: chain H residue 288 ARG Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 325 MET Chi-restraints excluded: chain J residue 340 TRP Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 227 MET Chi-restraints excluded: chain K residue 250 ILE Chi-restraints excluded: chain K residue 355 MET Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 173 HIS Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 351 THR Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 206 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 199 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 227 optimal weight: 0.8980 chunk 164 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 ASN ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 27978 Z= 0.349 Angle : 0.671 11.263 38036 Z= 0.329 Chirality : 0.045 0.200 4284 Planarity : 0.004 0.057 4891 Dihedral : 7.890 86.838 4016 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.49 % Allowed : 17.86 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.15), residues: 3433 helix: 0.69 (0.15), residues: 1384 sheet: -1.21 (0.21), residues: 588 loop : -1.54 (0.17), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 170 HIS 0.009 0.001 HIS H 339 PHE 0.036 0.002 PHE A 287 TYR 0.019 0.001 TYR K 188 ARG 0.008 0.001 ARG J 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 340 time to evaluate : 3.315 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: A 141 ASN cc_start: 0.9256 (t0) cc_final: 0.8850 (t0) REVERT: A 239 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.9008 (mmt-90) REVERT: B 28 GLN cc_start: 0.9038 (pp30) cc_final: 0.8726 (pp30) REVERT: B 113 VAL cc_start: 0.9204 (m) cc_final: 0.8976 (p) REVERT: B 127 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.7871 (m-80) REVERT: C 62 ASP cc_start: 0.8806 (t0) cc_final: 0.8450 (t0) REVERT: C 66 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8637 (mppt) REVERT: C 153 ASP cc_start: 0.8795 (t0) cc_final: 0.8412 (t0) REVERT: C 169 LYS cc_start: 0.9457 (mttt) cc_final: 0.9218 (mttm) REVERT: C 226 ASP cc_start: 0.8597 (t0) cc_final: 0.8244 (t0) REVERT: C 286 HIS cc_start: 0.9285 (OUTLIER) cc_final: 0.8062 (p-80) REVERT: D 157 MET cc_start: 0.6529 (tpp) cc_final: 0.6249 (tpp) REVERT: D 264 VAL cc_start: 0.8060 (m) cc_final: 0.7786 (p) REVERT: F 89 LYS cc_start: 0.8897 (tptp) cc_final: 0.8284 (tppp) REVERT: F 92 GLN cc_start: 0.9152 (tm-30) cc_final: 0.8738 (tm-30) REVERT: F 137 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8620 (mm-30) REVERT: G 27 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6881 (tp30) REVERT: G 151 ASP cc_start: 0.8564 (p0) cc_final: 0.8218 (p0) REVERT: H 243 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8511 (m-80) REVERT: H 248 GLU cc_start: 0.7511 (tp30) cc_final: 0.7199 (tp30) REVERT: H 260 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8331 (mm-40) REVERT: I 68 LYS cc_start: 0.8559 (mttt) cc_final: 0.8338 (mtmm) REVERT: I 107 GLU cc_start: 0.8029 (tt0) cc_final: 0.7758 (pt0) REVERT: I 283 MET cc_start: 0.9190 (mmp) cc_final: 0.8680 (mmp) REVERT: J 132 MET cc_start: 0.8769 (ppp) cc_final: 0.8464 (ppp) REVERT: J 261 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9136 (tt) REVERT: J 269 MET cc_start: 0.8542 (ptp) cc_final: 0.8244 (ptp) REVERT: J 288 ASP cc_start: 0.8217 (p0) cc_final: 0.7820 (p0) REVERT: K 123 MET cc_start: 0.8762 (tpp) cc_final: 0.8452 (tpp) REVERT: K 162 ASN cc_start: 0.8583 (OUTLIER) cc_final: 0.8127 (p0) REVERT: K 169 TYR cc_start: 0.7936 (m-80) cc_final: 0.7099 (t80) REVERT: K 217 CYS cc_start: 0.8760 (m) cc_final: 0.8075 (m) REVERT: K 316 GLU cc_start: 0.9060 (tp30) cc_final: 0.8726 (tp30) REVERT: L 92 ASN cc_start: 0.8396 (m110) cc_final: 0.8047 (m-40) REVERT: L 165 ILE cc_start: 0.8868 (mm) cc_final: 0.8599 (tp) REVERT: L 210 ARG cc_start: 0.8439 (tmm-80) cc_final: 0.8149 (ttp80) REVERT: L 263 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7036 (mt0) REVERT: L 360 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7829 (tm-30) outliers start: 99 outliers final: 74 residues processed: 412 average time/residue: 0.3546 time to fit residues: 240.0356 Evaluate side-chains 415 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 334 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 96 HIS Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 353 TYR Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 243 PHE Chi-restraints excluded: chain H residue 286 PHE Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 277 THR Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 281 SER Chi-restraints excluded: chain J residue 299 MET Chi-restraints excluded: chain J residue 340 TRP Chi-restraints excluded: chain J residue 354 GLN Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 227 MET Chi-restraints excluded: chain L residue 12 ASN Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 173 HIS Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 292 ASP Chi-restraints excluded: chain L residue 351 THR Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 303 optimal weight: 0.5980 chunk 319 optimal weight: 7.9990 chunk 291 optimal weight: 4.9990 chunk 310 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 135 optimal weight: 0.9980 chunk 244 optimal weight: 0.3980 chunk 95 optimal weight: 0.9990 chunk 280 optimal weight: 4.9990 chunk 293 optimal weight: 5.9990 chunk 309 optimal weight: 20.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 ASN I 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27978 Z= 0.218 Angle : 0.633 11.577 38036 Z= 0.306 Chirality : 0.044 0.192 4284 Planarity : 0.004 0.059 4891 Dihedral : 7.741 86.389 4016 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.78 % Allowed : 18.78 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.15), residues: 3433 helix: 0.74 (0.15), residues: 1380 sheet: -1.15 (0.21), residues: 589 loop : -1.52 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 170 HIS 0.008 0.001 HIS H 339 PHE 0.031 0.001 PHE A 287 TYR 0.028 0.001 TYR H 304 ARG 0.008 0.000 ARG L 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 345 time to evaluate : 3.307 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: A 239 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.8992 (mmt-90) REVERT: B 28 GLN cc_start: 0.9009 (pp30) cc_final: 0.8693 (pp30) REVERT: B 113 VAL cc_start: 0.9144 (m) cc_final: 0.8907 (p) REVERT: B 127 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.7764 (m-80) REVERT: C 62 ASP cc_start: 0.8744 (t0) cc_final: 0.8429 (t0) REVERT: C 66 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8570 (mppt) REVERT: C 153 ASP cc_start: 0.8763 (t0) cc_final: 0.8372 (t0) REVERT: C 169 LYS cc_start: 0.9424 (mttt) cc_final: 0.9182 (mttm) REVERT: C 226 ASP cc_start: 0.8560 (t0) cc_final: 0.8203 (t0) REVERT: C 286 HIS cc_start: 0.9249 (OUTLIER) cc_final: 0.8032 (p-80) REVERT: D 109 MET cc_start: 0.9067 (tpt) cc_final: 0.8637 (tpp) REVERT: D 157 MET cc_start: 0.6486 (tpp) cc_final: 0.6180 (tpp) REVERT: D 264 VAL cc_start: 0.7987 (m) cc_final: 0.7721 (p) REVERT: F 89 LYS cc_start: 0.8873 (tptp) cc_final: 0.8263 (tppp) REVERT: F 92 GLN cc_start: 0.9159 (tm-30) cc_final: 0.8766 (tm-30) REVERT: F 137 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8574 (mm-30) REVERT: G 27 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6906 (tp30) REVERT: G 151 ASP cc_start: 0.8543 (p0) cc_final: 0.8177 (p0) REVERT: H 243 PHE cc_start: 0.8988 (OUTLIER) cc_final: 0.8479 (m-80) REVERT: H 248 GLU cc_start: 0.7500 (tp30) cc_final: 0.7205 (tp30) REVERT: H 249 LYS cc_start: 0.8102 (tppt) cc_final: 0.7766 (tppt) REVERT: I 68 LYS cc_start: 0.8561 (mttt) cc_final: 0.8326 (mtmm) REVERT: I 107 GLU cc_start: 0.8031 (tt0) cc_final: 0.7754 (pt0) REVERT: I 283 MET cc_start: 0.9170 (mmp) cc_final: 0.8668 (mmp) REVERT: J 132 MET cc_start: 0.8754 (ppp) cc_final: 0.8450 (ppp) REVERT: J 165 ILE cc_start: 0.9529 (mp) cc_final: 0.9177 (mm) REVERT: J 261 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9080 (tt) REVERT: J 269 MET cc_start: 0.8505 (ptp) cc_final: 0.8238 (ptp) REVERT: K 16 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9074 (pp) REVERT: K 162 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.8054 (p0) REVERT: K 169 TYR cc_start: 0.7875 (m-80) cc_final: 0.7107 (t80) REVERT: K 217 CYS cc_start: 0.8729 (m) cc_final: 0.8013 (m) REVERT: K 283 MET cc_start: 0.9169 (mmm) cc_final: 0.8799 (mmm) REVERT: K 316 GLU cc_start: 0.9014 (tp30) cc_final: 0.8712 (tp30) REVERT: L 59 GLN cc_start: 0.8805 (tp40) cc_final: 0.8429 (tp40) REVERT: L 92 ASN cc_start: 0.8396 (m110) cc_final: 0.8043 (m-40) REVERT: L 137 GLN cc_start: 0.6609 (mt0) cc_final: 0.6177 (mp10) REVERT: L 165 ILE cc_start: 0.8831 (mm) cc_final: 0.8570 (tp) REVERT: L 210 ARG cc_start: 0.8427 (tmm-80) cc_final: 0.8134 (ttp80) REVERT: L 263 GLN cc_start: 0.7487 (mm-40) cc_final: 0.6788 (mt0) REVERT: L 360 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7850 (tm-30) outliers start: 79 outliers final: 63 residues processed: 405 average time/residue: 0.3552 time to fit residues: 234.6223 Evaluate side-chains 406 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 335 time to evaluate : 3.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 PHE Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 353 TYR Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain H residue 243 PHE Chi-restraints excluded: chain H residue 286 PHE Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 277 THR Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain J residue 281 SER Chi-restraints excluded: chain J residue 299 MET Chi-restraints excluded: chain J residue 340 TRP Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 227 MET Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 173 HIS Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 351 THR Chi-restraints excluded: chain L residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.0516 > 50: distance: 16 - 106: 10.804 distance: 19 - 103: 14.726 distance: 30 - 94: 3.645 distance: 33 - 91: 13.353 distance: 54 - 60: 4.581 distance: 60 - 61: 8.304 distance: 61 - 62: 4.460 distance: 61 - 64: 11.972 distance: 62 - 68: 5.318 distance: 64 - 65: 9.128 distance: 68 - 69: 4.017 distance: 69 - 70: 7.261 distance: 69 - 72: 9.987 distance: 70 - 71: 7.439 distance: 70 - 73: 15.468 distance: 73 - 74: 8.471 distance: 73 - 79: 23.796 distance: 74 - 75: 29.133 distance: 74 - 77: 8.014 distance: 75 - 76: 15.102 distance: 75 - 80: 25.753 distance: 77 - 78: 10.659 distance: 78 - 79: 17.168 distance: 80 - 81: 30.626 distance: 81 - 82: 51.052 distance: 81 - 84: 24.042 distance: 82 - 83: 26.080 distance: 82 - 91: 33.317 distance: 84 - 85: 16.172 distance: 85 - 86: 7.585 distance: 86 - 87: 8.065 distance: 87 - 88: 3.097 distance: 91 - 92: 33.088 distance: 92 - 93: 8.465 distance: 92 - 95: 24.001 distance: 93 - 94: 9.369 distance: 93 - 96: 10.671 distance: 96 - 97: 13.348 distance: 97 - 98: 15.182 distance: 97 - 100: 17.252 distance: 98 - 99: 17.220 distance: 98 - 103: 14.885 distance: 100 - 101: 12.405 distance: 100 - 102: 9.982 distance: 103 - 104: 11.351 distance: 104 - 105: 25.704 distance: 104 - 107: 33.206 distance: 105 - 106: 10.985 distance: 105 - 114: 14.288 distance: 107 - 108: 24.049 distance: 108 - 109: 25.780 distance: 108 - 110: 12.522 distance: 109 - 111: 13.227 distance: 110 - 112: 7.115 distance: 111 - 113: 13.034 distance: 112 - 113: 10.387 distance: 114 - 115: 15.286 distance: 114 - 120: 19.816 distance: 115 - 116: 11.209 distance: 115 - 118: 10.442 distance: 116 - 117: 18.055 distance: 116 - 121: 7.547 distance: 118 - 119: 16.549 distance: 119 - 120: 15.187 distance: 121 - 122: 22.064 distance: 122 - 123: 23.860 distance: 122 - 125: 18.237 distance: 123 - 124: 9.803 distance: 123 - 127: 14.677 distance: 125 - 126: 4.288 distance: 135 - 150: 3.148