Starting phenix.real_space_refine on Fri Mar 22 04:43:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psu_20464/03_2024/6psu_20464_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psu_20464/03_2024/6psu_20464.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/6psu_20464/03_2024/6psu_20464.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psu_20464/03_2024/6psu_20464.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psu_20464/03_2024/6psu_20464_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psu_20464/03_2024/6psu_20464_trim_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= 0.000 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: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 79 5.49 5 Mg 1 5.21 5 S 139 5.16 5 C 19952 2.51 5 N 5657 2.21 5 O 6336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 15": "OD1" <-> "OD2" Residue "G GLU 80": "OE1" <-> "OE2" Residue "G GLU 97": "OE1" <-> "OE2" Residue "G ASP 118": "OD1" <-> "OD2" Residue "G TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 164": "OD1" <-> "OD2" Residue "G ASP 174": "OD1" <-> "OD2" Residue "G ASP 199": "OD1" <-> "OD2" Residue "G ASP 212": "OD1" <-> "OD2" Residue "G PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 15": "OD1" <-> "OD2" Residue "H GLU 17": "OE1" <-> "OE2" Residue "H TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 188": "OE1" <-> "OE2" Residue "I TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 222": "OD1" <-> "OD2" Residue "I PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 244": "OE1" <-> "OE2" Residue "I GLU 264": "OE1" <-> "OE2" Residue "I ASP 320": "OD1" <-> "OD2" Residue "I PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 354": "OD1" <-> "OD2" Residue "I GLU 365": "OE1" <-> "OE2" Residue "I PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 441": "OE1" <-> "OE2" Residue "I ASP 446": "OD1" <-> "OD2" Residue "I GLU 461": "OE1" <-> "OE2" Residue "I GLU 546": "OE1" <-> "OE2" Residue "I TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 648": "OD1" <-> "OD2" Residue "I TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 711": "OD1" <-> "OD2" Residue "I TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 849": "OE1" <-> "OE2" Residue "I ASP 912": "OD1" <-> "OD2" Residue "I ASP 937": "OD1" <-> "OD2" Residue "I ASP 942": "OD1" <-> "OD2" Residue "I ASP 995": "OD1" <-> "OD2" Residue "I GLU 1012": "OE1" <-> "OE2" Residue "I ASP 1041": "OD1" <-> "OD2" Residue "I GLU 1143": "OE1" <-> "OE2" Residue "I ASP 1154": "OD1" <-> "OD2" Residue "I TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 1251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 1281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 1297": "OD1" <-> "OD2" Residue "I ASP 1341": "OD1" <-> "OD2" Residue "J GLU 16": "OE1" <-> "OE2" Residue "J PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 54": "OD1" <-> "OD2" Residue "J ARG 133": "NH1" <-> "NH2" Residue "J TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 163": "OE1" <-> "OE2" Residue "J ASP 174": "OD1" <-> "OD2" Residue "J PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 248": "OD1" <-> "OD2" Residue "J ARG 259": "NH1" <-> "NH2" Residue "J PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 505": "OD1" <-> "OD2" Residue "J ASP 558": "OD1" <-> "OD2" Residue "J TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 643": "OD1" <-> "OD2" Residue "J ASP 710": "OD1" <-> "OD2" Residue "J GLU 713": "OE1" <-> "OE2" Residue "J GLU 714": "OE1" <-> "OE2" Residue "J ARG 738": "NH1" <-> "NH2" Residue "J ARG 799": "NH1" <-> "NH2" Residue "J ASP 802": "OD1" <-> "OD2" Residue "J GLU 811": "OE1" <-> "OE2" Residue "J GLU 874": "OE1" <-> "OE2" Residue "J PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1066": "OE1" <-> "OE2" Residue "J ASP 1087": "OD1" <-> "OD2" Residue "J GLU 1110": "OE1" <-> "OE2" Residue "J ASP 1143": "OD1" <-> "OD2" Residue "J PHE 1165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1188": "OE1" <-> "OE2" Residue "J GLU 1205": "OE1" <-> "OE2" Residue "J ASP 1208": "OD1" <-> "OD2" Residue "J ASP 1212": "OD1" <-> "OD2" Residue "J TYR 1282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1293": "OE1" <-> "OE2" Residue "J GLU 1334": "OE1" <-> "OE2" Residue "J GLU 1343": "OE1" <-> "OE2" Residue "J GLU 1349": "OE1" <-> "OE2" Residue "K ASP 44": "OD1" <-> "OD2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "L GLU 42": "OE1" <-> "OE2" Residue "L ASP 43": "OD1" <-> "OD2" Residue "L ASP 75": "OD1" <-> "OD2" Residue "L GLU 116": "OE1" <-> "OE2" Residue "L PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 267": "OD1" <-> "OD2" Residue "L GLU 328": "OE1" <-> "OE2" Residue "L GLU 335": "OE1" <-> "OE2" Residue "L ASP 360": "OD1" <-> "OD2" Residue "L GLU 369": "OE1" <-> "OE2" Residue "L ASP 417": "OD1" <-> "OD2" Residue "L PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 476": "NH1" <-> "NH2" Residue "L GLU 485": "OE1" <-> "OE2" Residue "L ASP 513": "OD1" <-> "OD2" Residue "L ASP 516": "OD1" <-> "OD2" Residue "L PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 570": "OD1" <-> "OD2" Residue "L ARG 608": "NH1" <-> "NH2" Residue "L ASP 613": "OD1" <-> "OD2" Residue "M ASP 258": "OD1" <-> "OD2" Residue "M ASP 259": "OD1" <-> "OD2" Residue "M GLU 302": "OE1" <-> "OE2" Residue "M ASP 305": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32167 Number of models: 1 Model: "" Number of chains: 14 Chain: "N" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} Chain: "G" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1775 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 220} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1668 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1282} Chain: "J" Number of atoms: 10433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1344, 10433 Classifications: {'peptide': 1344} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 55, 'TRANS': 1288} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "K" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 577 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "L" Number of atoms: 4277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4277 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 513} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 863 Classifications: {'DNA': 42} Link IDs: {'rna3p': 41} Chain: "P" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 752 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "M" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 68} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, '1N7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 281 SG CYS N 37 56.648 57.288 28.905 1.00 53.14 S ATOM 301 SG CYS N 40 53.785 57.214 26.133 1.00 53.44 S ATOM 438 SG CYS N 58 57.291 59.428 26.238 1.00 43.23 S ATOM 460 SG CYS N 61 54.572 60.028 29.290 1.00 46.39 S ATOM 15030 SG CYS J 70 81.007 103.049 115.872 1.00 33.05 S ATOM 15152 SG CYS J 85 77.287 103.313 118.934 1.00 41.74 S ATOM 15176 SG CYS J 88 77.317 102.976 115.479 1.00 32.14 S ATOM 21411 SG CYS J 888 74.490 44.471 88.473 1.00 23.95 S ATOM 21483 SG CYS J 898 76.204 41.720 86.848 1.00 11.77 S Time building chain proxies: 17.43, per 1000 atoms: 0.54 Number of scatterers: 32167 At special positions: 0 Unit cell: (163.8, 157.3, 170.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 139 16.00 P 79 15.00 Mg 1 11.99 O 6336 8.00 N 5657 7.00 C 19952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.71 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 58 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 37 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 61 " Number of angles added : 6 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7206 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 140 helices and 32 sheets defined 36.8% alpha, 6.6% beta 33 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 16.44 Creating SS restraints... Processing helix chain 'N' and resid 4 through 25 removed outlier: 4.568A pdb=" N SER N 10 " --> pdb=" O ASP N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 51 Processing helix chain 'N' and resid 59 through 71 removed outlier: 3.866A pdb=" N HIS N 71 " --> pdb=" O ARG N 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 78 through 87 removed outlier: 4.168A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 155 through 158 No H-bonds generated for 'chain 'G' and resid 155 through 158' Processing helix chain 'G' and resid 213 through 233 removed outlier: 4.439A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 49 removed outlier: 3.752A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 86 Processing helix chain 'H' and resid 155 through 157 No H-bonds generated for 'chain 'H' and resid 155 through 157' Processing helix chain 'H' and resid 213 through 230 removed outlier: 3.547A pdb=" N THR H 222 " --> pdb=" O ARG H 218 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE H 223 " --> pdb=" O ARG H 219 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU H 224 " --> pdb=" O ALA H 220 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ALA H 230 " --> pdb=" O GLU H 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 9 removed outlier: 3.654A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 5 through 9' Processing helix chain 'I' and resid 27 through 35 removed outlier: 4.384A pdb=" N ILE I 30 " --> pdb=" O LEU I 27 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU I 32 " --> pdb=" O SER I 29 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP I 33 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 56 removed outlier: 3.836A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 206 through 212 Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 271 through 280 Processing helix chain 'I' and resid 319 through 328 removed outlier: 3.663A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 347 through 353 Processing helix chain 'I' and resid 360 through 370 Processing helix chain 'I' and resid 378 through 389 removed outlier: 3.899A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 392 through 394 No H-bonds generated for 'chain 'I' and resid 392 through 394' Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 422 through 436 removed outlier: 4.068A pdb=" N VAL I 428 " --> pdb=" O ASP I 424 " (cutoff:3.500A) Processing helix chain 'I' and resid 456 through 480 removed outlier: 3.639A pdb=" N VAL I 466 " --> pdb=" O ASN I 462 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY I 467 " --> pdb=" O GLN I 463 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 496 through 507 Processing helix chain 'I' and resid 520 through 526 Processing helix chain 'I' and resid 552 through 554 No H-bonds generated for 'chain 'I' and resid 552 through 554' Processing helix chain 'I' and resid 608 through 613 removed outlier: 4.556A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 613' Processing helix chain 'I' and resid 647 through 649 No H-bonds generated for 'chain 'I' and resid 647 through 649' Processing helix chain 'I' and resid 658 through 660 No H-bonds generated for 'chain 'I' and resid 658 through 660' Processing helix chain 'I' and resid 665 through 667 No H-bonds generated for 'chain 'I' and resid 665 through 667' Processing helix chain 'I' and resid 671 through 673 No H-bonds generated for 'chain 'I' and resid 671 through 673' Processing helix chain 'I' and resid 676 through 688 Processing helix chain 'I' and resid 705 through 710 Processing helix chain 'I' and resid 820 through 824 Processing helix chain 'I' and resid 859 through 862 No H-bonds generated for 'chain 'I' and resid 859 through 862' Processing helix chain 'I' and resid 900 through 905 Processing helix chain 'I' and resid 943 through 980 Processing helix chain 'I' and resid 988 through 991 No H-bonds generated for 'chain 'I' and resid 988 through 991' Processing helix chain 'I' and resid 994 through 996 No H-bonds generated for 'chain 'I' and resid 994 through 996' Processing helix chain 'I' and resid 1006 through 1037 Processing helix chain 'I' and resid 1100 through 1105 removed outlier: 4.022A pdb=" N VAL I1103 " --> pdb=" O PRO I1100 " (cutoff:3.500A) Proline residue: I1104 - end of helix No H-bonds generated for 'chain 'I' and resid 1100 through 1105' Processing helix chain 'I' and resid 1110 through 1133 Processing helix chain 'I' and resid 1139 through 1149 Processing helix chain 'I' and resid 1169 through 1174 Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1239 through 1241 No H-bonds generated for 'chain 'I' and resid 1239 through 1241' Processing helix chain 'I' and resid 1272 through 1280 Processing helix chain 'I' and resid 1285 through 1292 Processing helix chain 'I' and resid 1298 through 1309 removed outlier: 3.982A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1321 through 1332 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 59 through 62 No H-bonds generated for 'chain 'J' and resid 59 through 62' Processing helix chain 'J' and resid 95 through 99 Processing helix chain 'J' and resid 114 through 117 No H-bonds generated for 'chain 'J' and resid 114 through 117' Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 162 through 169 Processing helix chain 'J' and resid 182 through 191 Processing helix chain 'J' and resid 194 through 206 removed outlier: 3.509A pdb=" N ASN J 206 " --> pdb=" O ARG J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 230 removed outlier: 3.925A pdb=" N LYS J 215 " --> pdb=" O GLU J 211 " (cutoff:3.500A) Processing helix chain 'J' and resid 234 through 236 No H-bonds generated for 'chain 'J' and resid 234 through 236' Processing helix chain 'J' and resid 248 through 250 No H-bonds generated for 'chain 'J' and resid 248 through 250' Processing helix chain 'J' and resid 264 through 285 Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 328 through 330 No H-bonds generated for 'chain 'J' and resid 328 through 330' Processing helix chain 'J' and resid 370 through 376 Processing helix chain 'J' and resid 378 through 387 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 406 through 415 removed outlier: 3.738A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 433 No H-bonds generated for 'chain 'J' and resid 431 through 433' Processing helix chain 'J' and resid 451 through 457 removed outlier: 4.375A pdb=" N ALA J 455 " --> pdb=" O PRO J 451 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ALA J 456 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 483 Processing helix chain 'J' and resid 486 through 488 No H-bonds generated for 'chain 'J' and resid 486 through 488' Processing helix chain 'J' and resid 506 through 513 Processing helix chain 'J' and resid 530 through 538 Processing helix chain 'J' and resid 574 through 582 removed outlier: 3.863A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE J 582 " --> pdb=" O ILE J 578 " (cutoff:3.500A) Processing helix chain 'J' and resid 589 through 591 No H-bonds generated for 'chain 'J' and resid 589 through 591' Processing helix chain 'J' and resid 598 through 612 Processing helix chain 'J' and resid 615 through 635 Processing helix chain 'J' and resid 641 through 643 No H-bonds generated for 'chain 'J' and resid 641 through 643' Processing helix chain 'J' and resid 650 through 669 Processing helix chain 'J' and resid 675 through 702 removed outlier: 4.962A pdb=" N ASN J 680 " --> pdb=" O GLY J 676 " (cutoff:3.500A) Processing helix chain 'J' and resid 723 through 725 No H-bonds generated for 'chain 'J' and resid 723 through 725' Processing helix chain 'J' and resid 734 through 741 Processing helix chain 'J' and resid 769 through 786 removed outlier: 3.638A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) Processing helix chain 'J' and resid 795 through 804 removed outlier: 4.419A pdb=" N VAL J 803 " --> pdb=" O ARG J 799 " (cutoff:3.500A) Processing helix chain 'J' and resid 866 through 875 Processing helix chain 'J' and resid 896 through 899 No H-bonds generated for 'chain 'J' and resid 896 through 899' Processing helix chain 'J' and resid 915 through 929 Proline residue: J 926 - end of helix removed outlier: 4.020A pdb=" N GLN J 929 " --> pdb=" O GLU J 925 " (cutoff:3.500A) Processing helix chain 'J' and resid 1139 through 1144 Processing helix chain 'J' and resid 1217 through 1224 Processing helix chain 'J' and resid 1226 through 1244 removed outlier: 4.484A pdb=" N ASP J1239 " --> pdb=" O ASN J1235 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) Processing helix chain 'J' and resid 1251 through 1260 removed outlier: 3.534A pdb=" N VAL J1257 " --> pdb=" O ILE J1253 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN J1259 " --> pdb=" O VAL J1255 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1294 removed outlier: 4.106A pdb=" N ARG J1290 " --> pdb=" O LYS J1286 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU J1293 " --> pdb=" O ASN J1289 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA J1294 " --> pdb=" O ARG J1290 " (cutoff:3.500A) Processing helix chain 'J' and resid 1309 through 1314 removed outlier: 3.777A pdb=" N LEU J1314 " --> pdb=" O THR J1310 " (cutoff:3.500A) Processing helix chain 'J' and resid 1328 through 1337 removed outlier: 3.506A pdb=" N GLU J1334 " --> pdb=" O ARG J1330 " (cutoff:3.500A) Processing helix chain 'J' and resid 1347 through 1353 removed outlier: 3.790A pdb=" N VAL J1351 " --> pdb=" O LEU J1347 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE J1352 " --> pdb=" O LYS J1348 " (cutoff:3.500A) Processing helix chain 'J' and resid 1361 through 1372 removed outlier: 3.826A pdb=" N ALA J1364 " --> pdb=" O THR J1361 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR J1365 " --> pdb=" O GLY J1362 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS J1366 " --> pdb=" O TYR J1363 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP J1368 " --> pdb=" O TYR J1365 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 18 through 31 removed outlier: 3.647A pdb=" N ARG K 25 " --> pdb=" O LEU K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 56 Processing helix chain 'K' and resid 61 through 72 Processing helix chain 'L' and resid 9 through 19 Processing helix chain 'L' and resid 24 through 29 Processing helix chain 'L' and resid 40 through 50 removed outlier: 4.597A pdb=" N ASP L 50 " --> pdb=" O GLN L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 85 Processing helix chain 'L' and resid 97 through 107 removed outlier: 4.671A pdb=" N THR L 107 " --> pdb=" O ARG L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 136 Processing helix chain 'L' and resid 138 through 152 Processing helix chain 'L' and resid 214 through 229 Processing helix chain 'L' and resid 232 through 234 No H-bonds generated for 'chain 'L' and resid 232 through 234' Processing helix chain 'L' and resid 246 through 249 No H-bonds generated for 'chain 'L' and resid 246 through 249' Processing helix chain 'L' and resid 251 through 258 removed outlier: 3.664A pdb=" N GLN L 258 " --> pdb=" O GLU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 287 removed outlier: 3.906A pdb=" N LEU L 269 " --> pdb=" O GLN L 265 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP L 278 " --> pdb=" O ARG L 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 299 through 309 removed outlier: 3.520A pdb=" N THR L 307 " --> pdb=" O ILE L 303 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLY L 308 " --> pdb=" O THR L 304 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN L 309 " --> pdb=" O LEU L 305 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 321 No H-bonds generated for 'chain 'L' and resid 319 through 321' Processing helix chain 'L' and resid 327 through 330 Processing helix chain 'L' and resid 337 through 351 Processing helix chain 'L' and resid 355 through 392 removed outlier: 3.679A pdb=" N ALA L 382 " --> pdb=" O GLU L 378 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN L 383 " --> pdb=" O MET L 379 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU L 384 " --> pdb=" O VAL L 380 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 416 removed outlier: 3.501A pdb=" N GLY L 411 " --> pdb=" O GLU L 407 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL L 416 " --> pdb=" O LEU L 412 " (cutoff:3.500A) Processing helix chain 'L' and resid 421 through 423 No H-bonds generated for 'chain 'L' and resid 421 through 423' Processing helix chain 'L' and resid 427 through 443 removed outlier: 3.748A pdb=" N THR L 432 " --> pdb=" O SER L 428 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 454 through 474 removed outlier: 3.518A pdb=" N MET L 470 " --> pdb=" O ILE L 466 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU L 473 " --> pdb=" O GLN L 469 " (cutoff:3.500A) Processing helix chain 'L' and resid 480 through 486 Processing helix chain 'L' and resid 494 through 498 Processing helix chain 'L' and resid 519 through 522 Processing helix chain 'L' and resid 531 through 549 removed outlier: 3.887A pdb=" N SER L 539 " --> pdb=" O ALA L 535 " (cutoff:3.500A) Processing helix chain 'L' and resid 553 through 562 Processing helix chain 'L' and resid 573 through 579 Processing helix chain 'L' and resid 584 through 598 removed outlier: 4.267A pdb=" N ARG L 588 " --> pdb=" O ARG L 584 " (cutoff:3.500A) Processing helix chain 'L' and resid 605 through 610 removed outlier: 3.881A pdb=" N PHE L 610 " --> pdb=" O VAL L 606 " (cutoff:3.500A) Processing helix chain 'M' and resid 251 through 253 No H-bonds generated for 'chain 'M' and resid 251 through 253' Processing helix chain 'M' and resid 257 through 259 No H-bonds generated for 'chain 'M' and resid 257 through 259' Processing helix chain 'M' and resid 264 through 272 Processing helix chain 'M' and resid 278 through 281 No H-bonds generated for 'chain 'M' and resid 278 through 281' Processing helix chain 'M' and resid 286 through 290 Processing helix chain 'M' and resid 297 through 309 Processing sheet with id= A, first strand: chain 'G' and resid 23 through 25 Processing sheet with id= B, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.540A pdb=" N LYS G 104 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 187 through 189 Processing sheet with id= D, first strand: chain 'G' and resid 108 through 111 removed outlier: 4.026A pdb=" N GLY G 108 " --> pdb=" O LEU G 133 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 16 through 18 removed outlier: 3.854A pdb=" N GLU H 17 " --> pdb=" O LYS H 25 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 97 through 100 removed outlier: 3.567A pdb=" N VAL H 98 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 180 through 184 removed outlier: 6.418A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'I' and resid 93 through 95 Processing sheet with id= I, first strand: chain 'I' and resid 119 through 123 removed outlier: 3.618A pdb=" N LEU I 100 " --> pdb=" O GLN I 120 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'I' and resid 149 through 151 Processing sheet with id= K, first strand: chain 'I' and resid 156 through 158 removed outlier: 3.562A pdb=" N ASP I 158 " --> pdb=" O ASN I 173 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 228 through 231 Processing sheet with id= M, first strand: chain 'I' and resid 603 through 607 Processing sheet with id= N, first strand: chain 'I' and resid 633 through 637 removed outlier: 3.616A pdb=" N CYS I 636 " --> pdb=" O SER I 643 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 749 through 752 removed outlier: 5.763A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 757 through 759 removed outlier: 3.788A pdb=" N THR I 763 " --> pdb=" O SER I 759 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 798 through 801 Processing sheet with id= R, first strand: chain 'I' and resid 802 through 804 removed outlier: 6.367A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.465A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 815 through 817 removed outlier: 6.328A pdb=" N VAL I1075 " --> pdb=" O ILE I 816 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'I' and resid 927 through 931 removed outlier: 3.871A pdb=" N THR I 927 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TYR I1053 " --> pdb=" O ILE I 929 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 103 through 106 Processing sheet with id= W, first strand: chain 'J' and resid 350 through 352 removed outlier: 3.657A pdb=" N GLN J 435 " --> pdb=" O LEU J 423 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 547 through 554 Processing sheet with id= Y, first strand: chain 'J' and resid 820 through 822 removed outlier: 4.318A pdb=" N VAL J 880 " --> pdb=" O MET J 822 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 965 through 967 removed outlier: 4.175A pdb=" N VAL J 966 " --> pdb=" O VAL J 974 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL J 974 " --> pdb=" O VAL J 966 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'J' and resid 981 through 984 Processing sheet with id= AB, first strand: chain 'J' and resid 1033 through 1035 removed outlier: 3.689A pdb=" N GLY J1033 " --> pdb=" O ILE J1115 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 1049 through 1051 Processing sheet with id= AD, first strand: chain 'J' and resid 1077 through 1079 removed outlier: 3.611A pdb=" N LEU J1078 " --> pdb=" O TYR J1099 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR J1099 " --> pdb=" O LEU J1078 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'J' and resid 1163 through 1165 Processing sheet with id= AF, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.342A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 940 hydrogen bonds defined for protein. 2718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 12.70 Time building geometry restraints manager: 14.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10139 1.33 - 1.46: 6818 1.46 - 1.58: 15429 1.58 - 1.71: 172 1.71 - 1.83: 250 Bond restraints: 32808 Sorted by residual: bond pdb=" C19 1N7 L 701 " pdb=" C3 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.832 -0.300 2.00e-02 2.50e+03 2.26e+02 bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.828 -0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C19 1N7 N 102 " pdb=" C3 1N7 N 102 " ideal model delta sigma weight residual 1.532 1.826 -0.294 2.00e-02 2.50e+03 2.16e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.819 -0.287 2.00e-02 2.50e+03 2.06e+02 bond pdb=" C3 1N7 N 102 " pdb=" C4 1N7 N 102 " ideal model delta sigma weight residual 1.532 1.729 -0.197 2.00e-02 2.50e+03 9.73e+01 ... (remaining 32803 not shown) Histogram of bond angle deviations from ideal: 96.86 - 104.30: 745 104.30 - 111.74: 15830 111.74 - 119.18: 11532 119.18 - 126.63: 16065 126.63 - 134.07: 492 Bond angle restraints: 44664 Sorted by residual: angle pdb=" N GLU I1167 " pdb=" CA GLU I1167 " pdb=" C GLU I1167 " ideal model delta sigma weight residual 110.80 126.79 -15.99 2.13e+00 2.20e-01 5.64e+01 angle pdb=" N VAL H 14 " pdb=" CA VAL H 14 " pdb=" C VAL H 14 " ideal model delta sigma weight residual 113.20 107.60 5.60 9.60e-01 1.09e+00 3.41e+01 angle pdb=" C ASP I1166 " pdb=" N GLU I1167 " pdb=" CA GLU I1167 " ideal model delta sigma weight residual 121.54 132.50 -10.96 1.91e+00 2.74e-01 3.29e+01 angle pdb=" N ASP I 516 " pdb=" CA ASP I 516 " pdb=" C ASP I 516 " ideal model delta sigma weight residual 108.41 99.75 8.66 1.61e+00 3.86e-01 2.90e+01 angle pdb=" CA ARG I1156 " pdb=" C ARG I1156 " pdb=" N GLN I1157 " ideal model delta sigma weight residual 117.63 124.26 -6.63 1.25e+00 6.40e-01 2.81e+01 ... (remaining 44659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.71: 18857 28.71 - 57.42: 1243 57.42 - 86.14: 141 86.14 - 114.85: 7 114.85 - 143.56: 4 Dihedral angle restraints: 20252 sinusoidal: 9082 harmonic: 11170 Sorted by residual: dihedral pdb=" CA ASP I1166 " pdb=" C ASP I1166 " pdb=" N GLU I1167 " pdb=" CA GLU I1167 " ideal model delta harmonic sigma weight residual -180.00 -51.16 -128.84 0 5.00e+00 4.00e-02 6.64e+02 dihedral pdb=" CA ASP I1240 " pdb=" C ASP I1240 " pdb=" N ASP I1241 " pdb=" CA ASP I1241 " ideal model delta harmonic sigma weight residual 180.00 147.94 32.06 0 5.00e+00 4.00e-02 4.11e+01 dihedral pdb=" CA SER I1165 " pdb=" C SER I1165 " pdb=" N ASP I1166 " pdb=" CA ASP I1166 " ideal model delta harmonic sigma weight residual 180.00 148.27 31.73 0 5.00e+00 4.00e-02 4.03e+01 ... (remaining 20249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4113 0.060 - 0.120: 910 0.120 - 0.180: 88 0.180 - 0.240: 17 0.240 - 0.300: 2 Chirality restraints: 5130 Sorted by residual: chirality pdb=" CA ASP I 516 " pdb=" N ASP I 516 " pdb=" C ASP I 516 " pdb=" CB ASP I 516 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA GLU I1167 " pdb=" N GLU I1167 " pdb=" C GLU I1167 " pdb=" CB GLU I1167 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CG LEU J 783 " pdb=" CB LEU J 783 " pdb=" CD1 LEU J 783 " pdb=" CD2 LEU J 783 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 5127 not shown) Planarity restraints: 5537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY J 358 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO J 359 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO J 359 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO J 359 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN J 45 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.09e+00 pdb=" C ASN J 45 " -0.039 2.00e-02 2.50e+03 pdb=" O ASN J 45 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR J 46 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 342 " -0.010 2.00e-02 2.50e+03 2.00e-02 3.98e+00 pdb=" C ASP I 342 " 0.035 2.00e-02 2.50e+03 pdb=" O ASP I 342 " -0.013 2.00e-02 2.50e+03 pdb=" N HIS I 343 " -0.012 2.00e-02 2.50e+03 ... (remaining 5534 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.42: 235 2.42 - 3.04: 23013 3.04 - 3.66: 50685 3.66 - 4.28: 75511 4.28 - 4.90: 119186 Nonbonded interactions: 268630 Sorted by model distance: nonbonded pdb=" O ILE J 937 " pdb=" OD1 ASP J1133 " model vdw 1.805 3.040 nonbonded pdb=" OD2 ASP J 464 " pdb="MG MG J1501 " model vdw 1.954 2.170 nonbonded pdb=" OD1 ASP I 826 " pdb=" OG1 THR I 829 " model vdw 1.962 2.440 nonbonded pdb=" OH TYR J 679 " pdb=" O ILE J 754 " model vdw 2.012 2.440 nonbonded pdb=" OG1 THR I 589 " pdb=" OE1 GLN I 659 " model vdw 2.015 2.440 ... (remaining 268625 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 'G' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 158 or resid 171 through 232)) selection = (chain 'H' and (resid 5 through 228 or (resid 229 through 230 and (name N or nam \ e CA or name C or name O or name CB )) or resid 231 through 232)) } 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: 1.670 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: 0.520 Extract box with map and model: 6.900 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 97.850 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.120 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 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 : 0.009 0.300 32808 Z= 0.551 Angle : 0.941 15.992 44664 Z= 0.541 Chirality : 0.049 0.300 5130 Planarity : 0.005 0.061 5537 Dihedral : 17.893 143.560 13046 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 47.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.48 % Favored : 87.46 % Rotamer: Outliers : 0.24 % Allowed : 11.16 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.34 (0.11), residues: 3845 helix: -2.43 (0.10), residues: 1465 sheet: -3.56 (0.22), residues: 348 loop : -3.16 (0.12), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 807 HIS 0.010 0.002 HIS I1070 PHE 0.033 0.003 PHE N 52 TYR 0.021 0.003 TYR J 679 ARG 0.012 0.001 ARG J 259 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 674 time to evaluate : 4.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 75 GLN cc_start: 0.8229 (pp30) cc_final: 0.7893 (pp30) REVERT: H 10 LYS cc_start: 0.8653 (mmtp) cc_final: 0.8282 (tppt) REVERT: H 62 ASP cc_start: 0.5529 (m-30) cc_final: 0.5157 (p0) REVERT: H 199 ASP cc_start: 0.6752 (m-30) cc_final: 0.6550 (m-30) REVERT: I 227 LYS cc_start: 0.6453 (mmtt) cc_final: 0.5887 (ptpt) REVERT: I 422 LYS cc_start: 0.8024 (pptt) cc_final: 0.7539 (pttm) REVERT: I 436 ARG cc_start: 0.8077 (tpt90) cc_final: 0.7647 (tpt90) REVERT: I 462 ASN cc_start: 0.7566 (t0) cc_final: 0.7010 (t0) REVERT: I 468 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7371 (mt) REVERT: I 644 LEU cc_start: 0.8756 (mm) cc_final: 0.8351 (mp) REVERT: I 699 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8249 (tp) REVERT: I 865 LEU cc_start: 0.8871 (mm) cc_final: 0.8201 (mp) REVERT: I 1025 PHE cc_start: 0.6137 (m-10) cc_final: 0.5849 (m-10) REVERT: I 1174 GLU cc_start: 0.7077 (tp30) cc_final: 0.6862 (tp30) REVERT: I 1232 MET cc_start: 0.7911 (mmm) cc_final: 0.7682 (mmt) REVERT: I 1243 MET cc_start: 0.7416 (tmm) cc_final: 0.7036 (ttp) REVERT: I 1290 MET cc_start: 0.7791 (tpp) cc_final: 0.7351 (tpp) REVERT: J 133 ARG cc_start: 0.5298 (mmt180) cc_final: 0.4972 (mmm160) REVERT: J 180 MET cc_start: 0.6396 (ttm) cc_final: 0.6171 (ttm) REVERT: J 292 VAL cc_start: 0.8021 (m) cc_final: 0.7678 (t) REVERT: J 342 LEU cc_start: 0.8848 (tp) cc_final: 0.8532 (tp) REVERT: J 442 ILE cc_start: 0.8645 (mm) cc_final: 0.8286 (mm) REVERT: J 604 MET cc_start: 0.8417 (ttp) cc_final: 0.8030 (ttp) REVERT: J 679 TYR cc_start: 0.7034 (t80) cc_final: 0.6579 (t80) REVERT: J 936 HIS cc_start: 0.7123 (t70) cc_final: 0.6810 (m-70) REVERT: J 1340 LYS cc_start: 0.7717 (mmtt) cc_final: 0.7492 (tptp) REVERT: J 1352 ILE cc_start: 0.9002 (mm) cc_final: 0.8790 (mt) REVERT: K 35 LYS cc_start: 0.7636 (mptt) cc_final: 0.7429 (mmtp) REVERT: K 49 ILE cc_start: 0.8511 (mt) cc_final: 0.8186 (mt) REVERT: K 59 ILE cc_start: 0.6860 (mt) cc_final: 0.6316 (mt) REVERT: L 96 ASP cc_start: 0.6337 (m-30) cc_final: 0.5756 (m-30) REVERT: L 114 GLU cc_start: 0.6683 (mt-10) cc_final: 0.6269 (pm20) REVERT: L 312 SER cc_start: 0.7220 (m) cc_final: 0.6834 (t) REVERT: L 434 TRP cc_start: 0.7095 (m100) cc_final: 0.6847 (m100) REVERT: L 488 LEU cc_start: 0.7028 (mp) cc_final: 0.6173 (pt) REVERT: L 508 GLU cc_start: 0.7427 (mp0) cc_final: 0.7097 (mp0) REVERT: L 609 SER cc_start: 0.7803 (m) cc_final: 0.7347 (t) outliers start: 8 outliers final: 2 residues processed: 677 average time/residue: 0.4955 time to fit residues: 510.2632 Evaluate side-chains 460 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 456 time to evaluate : 3.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 3.9990 chunk 297 optimal weight: 7.9990 chunk 164 optimal weight: 0.2980 chunk 101 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 chunk 307 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 228 optimal weight: 0.8980 chunk 355 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 21 ASN G 18 GLN ** G 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN H 84 ASN H 132 HIS H 227 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 343 HIS I 387 ASN I 406 ASN ** I 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN I 932 GLN I1017 GLN I1116 HIS ** I1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1257 GLN I1268 GLN I1299 ASN J 158 GLN J 294 ASN ** J 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 489 ASN J 680 ASN J1049 GLN J1238 GLN K 29 GLN K 31 GLN L 8 GLN L 82 GLN L 128 ASN L 147 GLN L 246 GLN L 309 ASN L 362 ASN ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 446 GLN L 469 GLN ** L 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 579 GLN M 276 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32808 Z= 0.218 Angle : 0.670 8.294 44664 Z= 0.351 Chirality : 0.044 0.178 5130 Planarity : 0.004 0.044 5537 Dihedral : 15.948 140.626 5412 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.28 % Favored : 92.69 % Rotamer: Outliers : 3.26 % Allowed : 16.99 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.08 (0.12), residues: 3845 helix: -1.14 (0.12), residues: 1519 sheet: -2.91 (0.25), residues: 326 loop : -2.67 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 807 HIS 0.008 0.001 HIS I1070 PHE 0.015 0.002 PHE L 266 TYR 0.016 0.002 TYR G 185 ARG 0.007 0.001 ARG I 976 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 557 time to evaluate : 3.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 196 THR cc_start: 0.5460 (m) cc_final: 0.5249 (m) REVERT: H 212 ASP cc_start: 0.7622 (p0) cc_final: 0.7402 (p0) REVERT: I 254 ASP cc_start: 0.2907 (OUTLIER) cc_final: 0.2434 (p0) REVERT: I 321 LEU cc_start: 0.6643 (mt) cc_final: 0.6063 (tp) REVERT: I 377 THR cc_start: 0.4506 (OUTLIER) cc_final: 0.4219 (m) REVERT: I 422 LYS cc_start: 0.7644 (pptt) cc_final: 0.7287 (pttm) REVERT: I 435 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8057 (tt) REVERT: I 462 ASN cc_start: 0.7183 (t0) cc_final: 0.6730 (t0) REVERT: I 496 LYS cc_start: 0.7680 (tttt) cc_final: 0.7302 (pttt) REVERT: I 516 ASP cc_start: 0.7906 (t0) cc_final: 0.7663 (p0) REVERT: I 522 SER cc_start: 0.8694 (p) cc_final: 0.7066 (t) REVERT: I 644 LEU cc_start: 0.8502 (mm) cc_final: 0.8253 (mp) REVERT: I 653 MET cc_start: 0.7728 (ttp) cc_final: 0.7462 (ttp) REVERT: I 699 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8317 (tp) REVERT: I 704 MET cc_start: 0.7382 (mmm) cc_final: 0.6881 (mmm) REVERT: I 750 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8061 (pt) REVERT: I 865 LEU cc_start: 0.8705 (mm) cc_final: 0.8181 (mp) REVERT: I 949 GLU cc_start: 0.6005 (tp30) cc_final: 0.5744 (tp30) REVERT: I 1290 MET cc_start: 0.8188 (tpp) cc_final: 0.7734 (tpp) REVERT: J 42 GLU cc_start: 0.6466 (mp0) cc_final: 0.6040 (mt-10) REVERT: J 135 ILE cc_start: 0.7429 (mt) cc_final: 0.7076 (mt) REVERT: J 292 VAL cc_start: 0.8119 (OUTLIER) cc_final: 0.7847 (t) REVERT: J 479 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6520 (mt-10) REVERT: J 485 MET cc_start: 0.7909 (ttt) cc_final: 0.7648 (ttm) REVERT: J 679 TYR cc_start: 0.6648 (t80) cc_final: 0.6345 (t80) REVERT: J 788 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7855 (mp) REVERT: J 1144 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7834 (tt) REVERT: J 1189 MET cc_start: 0.7099 (mtt) cc_final: 0.6737 (mtt) REVERT: K 19 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6267 (tp) REVERT: K 42 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6531 (mt-10) REVERT: L 11 LEU cc_start: 0.6018 (tp) cc_final: 0.5753 (tt) REVERT: L 96 ASP cc_start: 0.5960 (m-30) cc_final: 0.5676 (m-30) REVERT: L 118 ASP cc_start: 0.6798 (m-30) cc_final: 0.5956 (t0) REVERT: L 230 VAL cc_start: 0.5883 (p) cc_final: 0.5666 (p) REVERT: L 291 CYS cc_start: 0.3218 (m) cc_final: 0.2859 (p) REVERT: L 312 SER cc_start: 0.7457 (m) cc_final: 0.6997 (t) REVERT: L 362 ASN cc_start: 0.4905 (OUTLIER) cc_final: 0.4658 (p0) outliers start: 108 outliers final: 56 residues processed: 621 average time/residue: 0.4413 time to fit residues: 436.2033 Evaluate side-chains 477 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 411 time to evaluate : 3.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 173 ASN Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 254 ASP Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 966 ILE Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1050 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 654 ILE Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1144 LEU Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1260 MET Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 272 SER Chi-restraints excluded: chain L residue 362 ASN Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 452 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 600 HIS Chi-restraints excluded: chain L residue 613 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 296 optimal weight: 0.6980 chunk 242 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 356 optimal weight: 0.7980 chunk 385 optimal weight: 6.9990 chunk 317 optimal weight: 3.9990 chunk 353 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 286 optimal weight: 7.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN H 147 GLN I 83 GLN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 238 GLN I 258 ASN ** I 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1268 GLN ** J 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J1010 GLN ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN ** L 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32808 Z= 0.286 Angle : 0.665 8.296 44664 Z= 0.348 Chirality : 0.045 0.239 5130 Planarity : 0.005 0.058 5537 Dihedral : 15.836 142.028 5408 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.76 % Favored : 91.21 % Rotamer: Outliers : 4.92 % Allowed : 20.07 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.60 (0.13), residues: 3845 helix: -0.79 (0.13), residues: 1517 sheet: -2.53 (0.25), residues: 342 loop : -2.37 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP L 315 HIS 0.008 0.001 HIS I1070 PHE 0.024 0.002 PHE J1325 TYR 0.017 0.002 TYR J 679 ARG 0.010 0.001 ARG J 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 451 time to evaluate : 3.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 3 TYR cc_start: 0.4994 (m-80) cc_final: 0.4745 (m-10) REVERT: I 245 ARG cc_start: 0.6172 (ttp80) cc_final: 0.5888 (ttp80) REVERT: I 284 LEU cc_start: 0.5930 (tp) cc_final: 0.5662 (tp) REVERT: I 321 LEU cc_start: 0.6778 (mt) cc_final: 0.5919 (tp) REVERT: I 434 ASP cc_start: 0.6172 (OUTLIER) cc_final: 0.5911 (p0) REVERT: I 462 ASN cc_start: 0.7285 (t0) cc_final: 0.6835 (t0) REVERT: I 496 LYS cc_start: 0.7758 (tttt) cc_final: 0.7320 (pttt) REVERT: I 568 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8083 (p0) REVERT: I 644 LEU cc_start: 0.8550 (mm) cc_final: 0.8239 (mp) REVERT: I 653 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7422 (ttp) REVERT: I 704 MET cc_start: 0.7329 (mmm) cc_final: 0.6917 (mmm) REVERT: I 750 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8153 (pt) REVERT: I 865 LEU cc_start: 0.8642 (mm) cc_final: 0.8152 (mp) REVERT: I 1107 MET cc_start: 0.7671 (mtm) cc_final: 0.7335 (mtm) REVERT: I 1290 MET cc_start: 0.8112 (tpp) cc_final: 0.7670 (tpp) REVERT: I 1314 GLN cc_start: 0.7484 (mm-40) cc_final: 0.7126 (mm-40) REVERT: J 78 LEU cc_start: 0.8402 (tp) cc_final: 0.7993 (tt) REVERT: J 147 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6457 (tp) REVERT: J 292 VAL cc_start: 0.8197 (OUTLIER) cc_final: 0.7852 (t) REVERT: J 312 ARG cc_start: 0.6553 (tpp-160) cc_final: 0.6251 (tpp-160) REVERT: J 340 GLN cc_start: 0.6121 (tm-30) cc_final: 0.5802 (tp40) REVERT: J 342 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8842 (tp) REVERT: J 361 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9073 (pp) REVERT: J 429 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8190 (mm) REVERT: J 479 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6684 (mt-10) REVERT: J 527 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8805 (mt) REVERT: J 631 TYR cc_start: 0.8252 (m-80) cc_final: 0.7493 (m-80) REVERT: J 679 TYR cc_start: 0.6829 (t80) cc_final: 0.6559 (t80) REVERT: J 707 ILE cc_start: 0.8273 (pt) cc_final: 0.7972 (mm) REVERT: J 785 ASP cc_start: 0.7274 (m-30) cc_final: 0.7062 (m-30) REVERT: J 788 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7773 (mp) REVERT: K 19 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6464 (tp) REVERT: K 42 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6232 (mt-10) REVERT: L 11 LEU cc_start: 0.5993 (tp) cc_final: 0.5731 (tt) REVERT: L 48 ILE cc_start: 0.4717 (OUTLIER) cc_final: 0.4492 (tt) REVERT: L 112 THR cc_start: 0.3635 (OUTLIER) cc_final: 0.3432 (t) REVERT: L 215 GLU cc_start: -0.0086 (OUTLIER) cc_final: -0.0584 (tp30) REVERT: L 356 GLU cc_start: 0.4655 (OUTLIER) cc_final: 0.4425 (tp30) REVERT: L 489 MET cc_start: 0.7393 (mmm) cc_final: 0.7165 (mmm) outliers start: 163 outliers final: 93 residues processed: 557 average time/residue: 0.4115 time to fit residues: 372.8131 Evaluate side-chains 503 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 394 time to evaluate : 3.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 226 GLU Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 485 ASP Chi-restraints excluded: chain I residue 568 ASN Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 654 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 752 ASN Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 916 SER Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 966 ILE Chi-restraints excluded: chain I residue 971 LEU Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1050 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 180 MET Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 495 ASN Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 654 ILE Chi-restraints excluded: chain J residue 714 GLU Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 908 ILE Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 215 GLU Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 356 GLU Chi-restraints excluded: chain L residue 459 THR Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 572 THR Chi-restraints excluded: chain L residue 600 HIS Chi-restraints excluded: chain L residue 613 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 8.9990 chunk 268 optimal weight: 8.9990 chunk 185 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 170 optimal weight: 0.9980 chunk 239 optimal weight: 9.9990 chunk 357 optimal weight: 2.9990 chunk 378 optimal weight: 20.0000 chunk 186 optimal weight: 4.9990 chunk 339 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 71 HIS H 66 HIS ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 238 GLN ** I 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 341 ASN ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN L 383 ASN ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 32808 Z= 0.340 Angle : 0.691 9.604 44664 Z= 0.361 Chirality : 0.045 0.217 5130 Planarity : 0.005 0.055 5537 Dihedral : 15.811 143.546 5408 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.26 % Favored : 90.72 % Rotamer: Outliers : 6.49 % Allowed : 21.33 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.42 (0.13), residues: 3845 helix: -0.70 (0.13), residues: 1510 sheet: -2.39 (0.24), residues: 382 loop : -2.19 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 315 HIS 0.008 0.001 HIS I1070 PHE 0.019 0.002 PHE N 52 TYR 0.018 0.002 TYR J 609 ARG 0.006 0.001 ARG J1304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 405 time to evaluate : 3.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 129 VAL cc_start: 0.8110 (OUTLIER) cc_final: 0.7873 (t) REVERT: I 238 GLN cc_start: 0.4420 (OUTLIER) cc_final: 0.4131 (tt0) REVERT: I 245 ARG cc_start: 0.6257 (ttp80) cc_final: 0.5944 (ttp80) REVERT: I 254 ASP cc_start: 0.2439 (OUTLIER) cc_final: 0.2136 (p0) REVERT: I 321 LEU cc_start: 0.7165 (mt) cc_final: 0.6062 (tp) REVERT: I 462 ASN cc_start: 0.7643 (t0) cc_final: 0.7199 (t0) REVERT: I 496 LYS cc_start: 0.7759 (tttt) cc_final: 0.7378 (pttt) REVERT: I 568 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8317 (p0) REVERT: I 653 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7465 (ttp) REVERT: I 704 MET cc_start: 0.7349 (mmm) cc_final: 0.7044 (mmm) REVERT: I 750 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8076 (pt) REVERT: I 865 LEU cc_start: 0.8693 (mm) cc_final: 0.8241 (mp) REVERT: I 1177 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.6869 (ttm170) REVERT: I 1240 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7394 (p0) REVERT: I 1314 GLN cc_start: 0.7580 (mm-40) cc_final: 0.7214 (mm-40) REVERT: J 78 LEU cc_start: 0.8448 (tp) cc_final: 0.8030 (tt) REVERT: J 134 ASP cc_start: 0.5111 (OUTLIER) cc_final: 0.4852 (t70) REVERT: J 147 ILE cc_start: 0.7106 (OUTLIER) cc_final: 0.6550 (tp) REVERT: J 255 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.6925 (tp) REVERT: J 292 VAL cc_start: 0.8197 (OUTLIER) cc_final: 0.7849 (t) REVERT: J 342 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8943 (tp) REVERT: J 349 TYR cc_start: 0.8556 (m-80) cc_final: 0.8335 (m-80) REVERT: J 361 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9049 (pp) REVERT: J 429 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8190 (mm) REVERT: J 527 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8862 (mt) REVERT: J 679 TYR cc_start: 0.7014 (t80) cc_final: 0.6690 (t80) REVERT: J 871 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7737 (tp) REVERT: K 42 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6336 (mt-10) REVERT: L 51 MET cc_start: 0.0201 (mmt) cc_final: -0.0534 (tpp) REVERT: L 112 THR cc_start: 0.3594 (OUTLIER) cc_final: 0.3375 (t) REVERT: L 118 ASP cc_start: 0.6438 (m-30) cc_final: 0.5773 (t0) REVERT: L 215 GLU cc_start: 0.0035 (OUTLIER) cc_final: -0.0546 (tp30) REVERT: L 264 LYS cc_start: 0.6621 (OUTLIER) cc_final: 0.6401 (pttm) REVERT: L 320 ILE cc_start: 0.0038 (OUTLIER) cc_final: -0.0460 (tt) outliers start: 215 outliers final: 131 residues processed: 562 average time/residue: 0.4073 time to fit residues: 377.7268 Evaluate side-chains 530 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 378 time to evaluate : 3.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 173 ASN Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 238 GLN Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 254 ASP Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 485 ASP Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 533 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 568 ASN Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 654 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 752 ASN Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 966 ILE Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1040 ASP Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1050 VAL Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1177 ARG Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 495 ASN Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 539 SER Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 654 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 714 GLU Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 870 ASP Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 908 ILE Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1052 GLU Chi-restraints excluded: chain J residue 1119 ASP Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 215 GLU Chi-restraints excluded: chain L residue 264 LYS Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 452 ILE Chi-restraints excluded: chain L residue 459 THR Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 572 THR Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 600 HIS Chi-restraints excluded: chain L residue 613 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 0.7980 chunk 215 optimal weight: 0.0670 chunk 5 optimal weight: 2.9990 chunk 282 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 323 optimal weight: 6.9990 chunk 261 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 193 optimal weight: 1.9990 chunk 340 optimal weight: 20.0000 chunk 95 optimal weight: 0.9980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 766 ASN ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 GLN ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32808 Z= 0.173 Angle : 0.595 9.765 44664 Z= 0.311 Chirality : 0.042 0.191 5130 Planarity : 0.004 0.052 5537 Dihedral : 15.407 143.012 5408 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.97 % Favored : 93.00 % Rotamer: Outliers : 4.47 % Allowed : 23.75 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.97 (0.13), residues: 3845 helix: -0.30 (0.13), residues: 1520 sheet: -2.04 (0.26), residues: 360 loop : -2.00 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 315 HIS 0.004 0.001 HIS L 30 PHE 0.024 0.001 PHE J 172 TYR 0.017 0.001 TYR L 268 ARG 0.003 0.000 ARG J 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 452 time to evaluate : 3.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 129 VAL cc_start: 0.7968 (p) cc_final: 0.7657 (t) REVERT: H 194 GLN cc_start: 0.6571 (mt0) cc_final: 0.6338 (mt0) REVERT: I 245 ARG cc_start: 0.5997 (ttp80) cc_final: 0.5607 (ttp80) REVERT: I 254 ASP cc_start: 0.2273 (OUTLIER) cc_final: 0.1955 (p0) REVERT: I 321 LEU cc_start: 0.6959 (mt) cc_final: 0.6094 (tp) REVERT: I 432 LEU cc_start: 0.8455 (tp) cc_final: 0.8232 (tp) REVERT: I 436 ARG cc_start: 0.7835 (tpt90) cc_final: 0.7589 (tpt90) REVERT: I 496 LYS cc_start: 0.7722 (tttt) cc_final: 0.7312 (pttt) REVERT: I 653 MET cc_start: 0.7486 (ttp) cc_final: 0.7180 (ttp) REVERT: I 685 MET cc_start: 0.7448 (mpp) cc_final: 0.7033 (mpp) REVERT: I 704 MET cc_start: 0.7260 (mmm) cc_final: 0.6792 (mmm) REVERT: I 733 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8716 (m) REVERT: I 865 LEU cc_start: 0.8603 (mm) cc_final: 0.8124 (mp) REVERT: I 1272 GLU cc_start: 0.7653 (tp30) cc_final: 0.7408 (tp30) REVERT: J 42 GLU cc_start: 0.6025 (OUTLIER) cc_final: 0.5810 (mt-10) REVERT: J 134 ASP cc_start: 0.5057 (OUTLIER) cc_final: 0.4746 (t70) REVERT: J 137 ARG cc_start: 0.6525 (mpt-90) cc_final: 0.6277 (mpt-90) REVERT: J 147 ILE cc_start: 0.7123 (OUTLIER) cc_final: 0.6593 (tp) REVERT: J 255 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7003 (tp) REVERT: J 292 VAL cc_start: 0.8142 (OUTLIER) cc_final: 0.7854 (t) REVERT: J 340 GLN cc_start: 0.6294 (tm-30) cc_final: 0.5852 (tp40) REVERT: J 342 LEU cc_start: 0.9162 (tp) cc_final: 0.8866 (mt) REVERT: J 429 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8054 (mm) REVERT: J 485 MET cc_start: 0.7856 (ttt) cc_final: 0.7628 (ttp) REVERT: J 631 TYR cc_start: 0.8275 (m-80) cc_final: 0.7554 (m-80) REVERT: J 679 TYR cc_start: 0.6680 (t80) cc_final: 0.6449 (t80) REVERT: J 707 ILE cc_start: 0.8369 (pt) cc_final: 0.7872 (mm) REVERT: J 714 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6160 (tt0) REVERT: J 788 LEU cc_start: 0.7776 (tt) cc_final: 0.7428 (mp) REVERT: J 995 TYR cc_start: 0.5970 (OUTLIER) cc_final: 0.5669 (m-80) REVERT: K 19 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6511 (tp) REVERT: K 42 GLU cc_start: 0.6780 (mt-10) cc_final: 0.6413 (mt-10) REVERT: L 11 LEU cc_start: 0.5783 (tp) cc_final: 0.5522 (tt) REVERT: L 264 LYS cc_start: 0.6508 (OUTLIER) cc_final: 0.6281 (pttm) REVERT: L 320 ILE cc_start: -0.0005 (OUTLIER) cc_final: -0.0470 (tt) REVERT: L 488 LEU cc_start: 0.6891 (mm) cc_final: 0.6169 (pt) REVERT: L 580 PHE cc_start: 0.4241 (OUTLIER) cc_final: 0.3598 (m-10) outliers start: 148 outliers final: 77 residues processed: 556 average time/residue: 0.4110 time to fit residues: 375.0367 Evaluate side-chains 475 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 385 time to evaluate : 3.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 173 ASN Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 254 ASP Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1198 LEU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 995 TYR Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1035 VAL Chi-restraints excluded: chain J residue 1119 ASP Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 264 LYS Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 580 PHE Chi-restraints excluded: chain L residue 600 HIS Chi-restraints excluded: chain L residue 613 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 0.0470 chunk 341 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 222 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 379 optimal weight: 20.0000 chunk 314 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 31 optimal weight: 0.0870 chunk 125 optimal weight: 2.9990 chunk 199 optimal weight: 9.9990 overall best weight: 2.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS I 238 GLN I 573 ASN I 766 ASN I1268 GLN ** J 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 32808 Z= 0.255 Angle : 0.630 9.858 44664 Z= 0.327 Chirality : 0.043 0.167 5130 Planarity : 0.004 0.048 5537 Dihedral : 15.407 144.423 5408 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.14 % Favored : 91.83 % Rotamer: Outliers : 5.49 % Allowed : 23.93 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.89 (0.13), residues: 3845 helix: -0.21 (0.13), residues: 1508 sheet: -2.07 (0.24), residues: 388 loop : -1.94 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 433 HIS 0.007 0.001 HIS I 673 PHE 0.016 0.001 PHE N 52 TYR 0.015 0.001 TYR J 349 ARG 0.004 0.000 ARG I 974 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 407 time to evaluate : 3.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 76 GLU cc_start: 0.8307 (mp0) cc_final: 0.8018 (mp0) REVERT: G 143 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6629 (mtp85) REVERT: H 129 VAL cc_start: 0.7991 (OUTLIER) cc_final: 0.7745 (t) REVERT: I 245 ARG cc_start: 0.5990 (ttp80) cc_final: 0.5715 (ttp80) REVERT: I 254 ASP cc_start: 0.2399 (OUTLIER) cc_final: 0.2041 (p0) REVERT: I 436 ARG cc_start: 0.7784 (tpt90) cc_final: 0.7560 (tpt90) REVERT: I 496 LYS cc_start: 0.7720 (tttt) cc_final: 0.7312 (pttt) REVERT: I 653 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7171 (ttp) REVERT: I 685 MET cc_start: 0.7417 (mpp) cc_final: 0.6989 (mpp) REVERT: I 733 VAL cc_start: 0.9053 (OUTLIER) cc_final: 0.8814 (m) REVERT: I 750 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7932 (pt) REVERT: I 865 LEU cc_start: 0.8659 (mm) cc_final: 0.8166 (mp) REVERT: I 1272 GLU cc_start: 0.7651 (tp30) cc_final: 0.7421 (tp30) REVERT: J 78 LEU cc_start: 0.8266 (tp) cc_final: 0.7953 (tt) REVERT: J 134 ASP cc_start: 0.5151 (OUTLIER) cc_final: 0.4867 (t70) REVERT: J 137 ARG cc_start: 0.6536 (mpt-90) cc_final: 0.6288 (mpt-90) REVERT: J 147 ILE cc_start: 0.7117 (OUTLIER) cc_final: 0.6573 (tp) REVERT: J 255 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.6948 (tp) REVERT: J 292 VAL cc_start: 0.8183 (OUTLIER) cc_final: 0.7888 (t) REVERT: J 342 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8906 (tp) REVERT: J 361 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8982 (pp) REVERT: J 429 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8147 (mm) REVERT: J 527 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8839 (mt) REVERT: J 631 TYR cc_start: 0.8305 (m-80) cc_final: 0.7553 (m-80) REVERT: J 707 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8082 (mm) REVERT: J 714 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6229 (tt0) REVERT: J 788 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7468 (mp) REVERT: K 19 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6548 (tp) REVERT: K 71 GLU cc_start: 0.6112 (tm-30) cc_final: 0.5830 (tm-30) REVERT: L 11 LEU cc_start: 0.5797 (tp) cc_final: 0.5508 (tt) REVERT: L 320 ILE cc_start: 0.0194 (OUTLIER) cc_final: -0.0188 (tt) REVERT: L 322 MET cc_start: 0.2196 (tmm) cc_final: 0.1938 (ppp) REVERT: L 513 ASP cc_start: 0.4051 (OUTLIER) cc_final: 0.3070 (t0) REVERT: L 580 PHE cc_start: 0.4748 (OUTLIER) cc_final: 0.3909 (m-10) outliers start: 182 outliers final: 119 residues processed: 536 average time/residue: 0.4105 time to fit residues: 360.3026 Evaluate side-chains 519 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 379 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 173 ASN Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 254 ASP Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 485 ASP Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 568 ASN Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 916 SER Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1040 ASP Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1050 VAL Chi-restraints excluded: chain I residue 1105 SER Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1198 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 329 ASP Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 495 ASN Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 654 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 714 GLU Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 870 ASP Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 922 SER Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1035 VAL Chi-restraints excluded: chain J residue 1119 ASP Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 513 ASP Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 580 PHE Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 600 HIS Chi-restraints excluded: chain L residue 613 ASP Chi-restraints excluded: chain M residue 288 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 216 optimal weight: 0.9990 chunk 276 optimal weight: 0.3980 chunk 214 optimal weight: 2.9990 chunk 319 optimal weight: 0.0050 chunk 211 optimal weight: 0.6980 chunk 377 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 chunk 230 optimal weight: 0.8980 chunk 174 optimal weight: 0.9980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1268 GLN ** J 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 GLN L 28 ASN ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 32808 Z= 0.157 Angle : 0.583 11.657 44664 Z= 0.303 Chirality : 0.041 0.191 5130 Planarity : 0.004 0.047 5537 Dihedral : 15.180 143.300 5408 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.16 % Favored : 93.81 % Rotamer: Outliers : 4.07 % Allowed : 25.74 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.13), residues: 3845 helix: 0.02 (0.13), residues: 1522 sheet: -1.93 (0.25), residues: 392 loop : -1.84 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 807 HIS 0.007 0.001 HIS I 673 PHE 0.026 0.001 PHE J 172 TYR 0.017 0.001 TYR J 349 ARG 0.007 0.000 ARG J 297 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 436 time to evaluate : 3.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 143 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6509 (mtp85) REVERT: H 129 VAL cc_start: 0.7979 (OUTLIER) cc_final: 0.7721 (t) REVERT: I 11 ILE cc_start: 0.8639 (tp) cc_final: 0.8406 (pt) REVERT: I 245 ARG cc_start: 0.5843 (ttp80) cc_final: 0.5567 (ttp80) REVERT: I 254 ASP cc_start: 0.2813 (OUTLIER) cc_final: 0.2495 (p0) REVERT: I 434 ASP cc_start: 0.6462 (OUTLIER) cc_final: 0.6128 (p0) REVERT: I 436 ARG cc_start: 0.7721 (tpt90) cc_final: 0.7504 (tpt90) REVERT: I 653 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7090 (ttp) REVERT: I 685 MET cc_start: 0.7361 (mpp) cc_final: 0.7022 (mpp) REVERT: I 733 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8688 (m) REVERT: I 865 LEU cc_start: 0.8586 (mm) cc_final: 0.8123 (mp) REVERT: J 134 ASP cc_start: 0.5020 (OUTLIER) cc_final: 0.4598 (t70) REVERT: J 147 ILE cc_start: 0.6809 (OUTLIER) cc_final: 0.6414 (tp) REVERT: J 255 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7041 (tp) REVERT: J 292 VAL cc_start: 0.7864 (OUTLIER) cc_final: 0.7586 (t) REVERT: J 340 GLN cc_start: 0.6617 (tm-30) cc_final: 0.6270 (tp40) REVERT: J 341 ASN cc_start: 0.7441 (m110) cc_final: 0.7203 (m-40) REVERT: J 342 LEU cc_start: 0.9078 (tp) cc_final: 0.8801 (mt) REVERT: J 361 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8928 (pp) REVERT: J 429 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.7902 (mm) REVERT: J 485 MET cc_start: 0.7786 (ttt) cc_final: 0.7514 (ttp) REVERT: J 527 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8809 (mt) REVERT: J 631 TYR cc_start: 0.8219 (m-80) cc_final: 0.7679 (m-80) REVERT: J 707 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7825 (mm) REVERT: J 788 LEU cc_start: 0.7751 (tt) cc_final: 0.7468 (mp) REVERT: K 19 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6247 (tp) REVERT: L 11 LEU cc_start: 0.5717 (tp) cc_final: 0.5498 (tt) REVERT: L 56 MET cc_start: 0.2320 (mmp) cc_final: 0.1539 (tpt) REVERT: L 320 ILE cc_start: 0.0121 (OUTLIER) cc_final: -0.0296 (tt) REVERT: L 322 MET cc_start: 0.1776 (tmm) cc_final: 0.1380 (ppp) REVERT: L 488 LEU cc_start: 0.6330 (mm) cc_final: 0.5703 (pt) REVERT: L 580 PHE cc_start: 0.4992 (OUTLIER) cc_final: 0.4282 (m-10) REVERT: L 595 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.5956 (mp) outliers start: 135 outliers final: 76 residues processed: 527 average time/residue: 0.4132 time to fit residues: 356.9616 Evaluate side-chains 473 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 379 time to evaluate : 3.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 173 ASN Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 254 ASP Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 916 SER Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1035 VAL Chi-restraints excluded: chain J residue 1119 ASP Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 513 ASP Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 580 PHE Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 591 GLU Chi-restraints excluded: chain L residue 595 LEU Chi-restraints excluded: chain L residue 600 HIS Chi-restraints excluded: chain M residue 288 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 0.0670 chunk 150 optimal weight: 9.9990 chunk 225 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 240 optimal weight: 5.9990 chunk 257 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 296 optimal weight: 1.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 739 GLN ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32808 Z= 0.175 Angle : 0.587 11.454 44664 Z= 0.303 Chirality : 0.041 0.188 5130 Planarity : 0.004 0.054 5537 Dihedral : 15.115 143.723 5408 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.89 % Allowed : 25.98 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.51 (0.13), residues: 3845 helix: 0.19 (0.13), residues: 1518 sheet: -1.84 (0.25), residues: 410 loop : -1.81 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 807 HIS 0.006 0.001 HIS I 673 PHE 0.019 0.001 PHE I 253 TYR 0.023 0.001 TYR H 68 ARG 0.006 0.000 ARG N 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 400 time to evaluate : 3.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 143 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6474 (mtp85) REVERT: H 129 VAL cc_start: 0.7967 (OUTLIER) cc_final: 0.7738 (t) REVERT: I 245 ARG cc_start: 0.6021 (ttp80) cc_final: 0.5704 (ttp80) REVERT: I 254 ASP cc_start: 0.2906 (OUTLIER) cc_final: 0.2546 (p0) REVERT: I 284 LEU cc_start: 0.4464 (OUTLIER) cc_final: 0.4013 (pt) REVERT: I 434 ASP cc_start: 0.6694 (OUTLIER) cc_final: 0.6307 (p0) REVERT: I 436 ARG cc_start: 0.7699 (tpt90) cc_final: 0.7291 (tpt90) REVERT: I 653 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7074 (ttp) REVERT: I 685 MET cc_start: 0.7061 (mpp) cc_final: 0.6468 (mmm) REVERT: I 733 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8749 (m) REVERT: I 750 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7743 (pt) REVERT: I 865 LEU cc_start: 0.8629 (mm) cc_final: 0.8162 (mp) REVERT: J 134 ASP cc_start: 0.5021 (OUTLIER) cc_final: 0.4601 (t70) REVERT: J 147 ILE cc_start: 0.6924 (OUTLIER) cc_final: 0.6560 (tp) REVERT: J 292 VAL cc_start: 0.8026 (OUTLIER) cc_final: 0.7727 (t) REVERT: J 340 GLN cc_start: 0.6608 (tm-30) cc_final: 0.6287 (tp40) REVERT: J 342 LEU cc_start: 0.9120 (tp) cc_final: 0.8824 (mt) REVERT: J 429 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.7997 (mm) REVERT: J 485 MET cc_start: 0.7806 (ttt) cc_final: 0.7567 (ttp) REVERT: J 527 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8843 (mt) REVERT: J 631 TYR cc_start: 0.8221 (m-80) cc_final: 0.7735 (m-80) REVERT: J 788 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7486 (mp) REVERT: K 19 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6220 (tp) REVERT: K 35 LYS cc_start: 0.7368 (mptt) cc_final: 0.7152 (mmtp) REVERT: L 56 MET cc_start: 0.1999 (mmp) cc_final: 0.1369 (tpt) REVERT: L 320 ILE cc_start: 0.0035 (OUTLIER) cc_final: -0.0336 (tt) REVERT: L 322 MET cc_start: 0.1709 (OUTLIER) cc_final: 0.1309 (ppp) REVERT: L 580 PHE cc_start: 0.5064 (OUTLIER) cc_final: 0.4381 (m-10) REVERT: L 595 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.5963 (mp) outliers start: 129 outliers final: 90 residues processed: 490 average time/residue: 0.4162 time to fit residues: 334.0252 Evaluate side-chains 475 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 366 time to evaluate : 3.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 173 ASN Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 254 ASP Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 916 SER Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1198 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 495 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 564 VAL Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1050 THR Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1119 ASP Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 322 MET Chi-restraints excluded: chain L residue 361 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 513 ASP Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 580 PHE Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 591 GLU Chi-restraints excluded: chain L residue 595 LEU Chi-restraints excluded: chain L residue 600 HIS Chi-restraints excluded: chain M residue 288 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 7.9990 chunk 361 optimal weight: 5.9990 chunk 330 optimal weight: 0.0570 chunk 352 optimal weight: 8.9990 chunk 211 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 chunk 276 optimal weight: 0.0980 chunk 108 optimal weight: 0.9980 chunk 318 optimal weight: 1.9990 chunk 332 optimal weight: 0.9990 chunk 350 optimal weight: 4.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 HIS I 330 HIS I 955 GLN ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 739 GLN J1289 ASN ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32808 Z= 0.159 Angle : 0.580 12.114 44664 Z= 0.299 Chirality : 0.041 0.184 5130 Planarity : 0.004 0.051 5537 Dihedral : 15.002 143.130 5408 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.19 % Favored : 93.78 % Rotamer: Outliers : 3.71 % Allowed : 26.31 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.35 (0.14), residues: 3845 helix: 0.34 (0.13), residues: 1516 sheet: -1.75 (0.25), residues: 394 loop : -1.73 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 807 HIS 0.006 0.001 HIS I 673 PHE 0.025 0.001 PHE J 172 TYR 0.016 0.001 TYR I1149 ARG 0.005 0.000 ARG N 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 412 time to evaluate : 3.706 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: G 143 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6861 (mtp85) REVERT: H 129 VAL cc_start: 0.7969 (OUTLIER) cc_final: 0.7732 (t) REVERT: I 245 ARG cc_start: 0.5847 (ttp80) cc_final: 0.5591 (ttp80) REVERT: I 254 ASP cc_start: 0.2829 (OUTLIER) cc_final: 0.2475 (p0) REVERT: I 289 VAL cc_start: 0.5611 (OUTLIER) cc_final: 0.5409 (p) REVERT: I 434 ASP cc_start: 0.6554 (OUTLIER) cc_final: 0.6142 (p0) REVERT: I 436 ARG cc_start: 0.7780 (tpt90) cc_final: 0.7374 (tpt90) REVERT: I 516 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6843 (p0) REVERT: I 685 MET cc_start: 0.6997 (mpp) cc_final: 0.6624 (mmm) REVERT: I 733 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8746 (m) REVERT: I 750 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7690 (pt) REVERT: I 865 LEU cc_start: 0.8564 (mm) cc_final: 0.8116 (mp) REVERT: J 134 ASP cc_start: 0.5008 (OUTLIER) cc_final: 0.4560 (t70) REVERT: J 147 ILE cc_start: 0.7049 (OUTLIER) cc_final: 0.6713 (tp) REVERT: J 292 VAL cc_start: 0.7860 (m) cc_final: 0.7565 (t) REVERT: J 341 ASN cc_start: 0.7577 (m110) cc_final: 0.7360 (t0) REVERT: J 342 LEU cc_start: 0.9089 (tp) cc_final: 0.8737 (mt) REVERT: J 429 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7884 (mm) REVERT: J 485 MET cc_start: 0.7749 (ttt) cc_final: 0.7524 (ttp) REVERT: J 527 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8881 (mt) REVERT: J 631 TYR cc_start: 0.8045 (m-80) cc_final: 0.7782 (m-80) REVERT: J 788 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7463 (mp) REVERT: J 867 GLN cc_start: 0.6125 (mp10) cc_final: 0.5741 (tm-30) REVERT: J 1244 GLN cc_start: 0.7953 (tp-100) cc_final: 0.7511 (mm110) REVERT: K 19 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6170 (tp) REVERT: K 35 LYS cc_start: 0.7304 (mptt) cc_final: 0.7008 (mttt) REVERT: L 56 MET cc_start: 0.2308 (mmp) cc_final: 0.1414 (tpt) REVERT: L 102 MET cc_start: 0.7508 (mmt) cc_final: 0.7259 (mpp) REVERT: L 320 ILE cc_start: -0.0518 (OUTLIER) cc_final: -0.0748 (tt) REVERT: L 322 MET cc_start: 0.1692 (OUTLIER) cc_final: 0.1467 (ppp) REVERT: L 476 ARG cc_start: 0.5289 (ptt90) cc_final: 0.4894 (ttp-170) REVERT: L 580 PHE cc_start: 0.5059 (OUTLIER) cc_final: 0.4417 (m-10) REVERT: L 595 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.5891 (mp) outliers start: 123 outliers final: 81 residues processed: 502 average time/residue: 0.4183 time to fit residues: 341.9016 Evaluate side-chains 476 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 377 time to evaluate : 3.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 173 ASN Chi-restraints excluded: chain I residue 254 ASP Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 916 SER Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1136 GLN Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1198 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 564 VAL Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1050 THR Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1119 ASP Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 322 MET Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 513 ASP Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 580 PHE Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 591 GLU Chi-restraints excluded: chain L residue 595 LEU Chi-restraints excluded: chain M residue 288 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 0.9980 chunk 372 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 176 optimal weight: 0.5980 chunk 258 optimal weight: 0.9990 chunk 390 optimal weight: 6.9990 chunk 359 optimal weight: 6.9990 chunk 310 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 240 optimal weight: 7.9990 chunk 190 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 HIS I 330 HIS ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1264 GLN ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32808 Z= 0.172 Angle : 0.586 12.645 44664 Z= 0.302 Chirality : 0.041 0.208 5130 Planarity : 0.004 0.051 5537 Dihedral : 14.925 143.611 5408 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.66 % Favored : 93.32 % Rotamer: Outliers : 3.14 % Allowed : 27.37 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.28 (0.14), residues: 3845 helix: 0.39 (0.13), residues: 1524 sheet: -1.74 (0.25), residues: 394 loop : -1.70 (0.14), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 807 HIS 0.009 0.001 HIS J 113 PHE 0.019 0.001 PHE I 253 TYR 0.016 0.001 TYR J 349 ARG 0.007 0.000 ARG L 363 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 387 time to evaluate : 3.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 143 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6862 (mtp85) REVERT: I 245 ARG cc_start: 0.5834 (ttp80) cc_final: 0.5602 (ttp80) REVERT: I 254 ASP cc_start: 0.2873 (OUTLIER) cc_final: 0.2503 (p0) REVERT: I 434 ASP cc_start: 0.6625 (OUTLIER) cc_final: 0.6231 (p0) REVERT: I 436 ARG cc_start: 0.7794 (tpt90) cc_final: 0.7398 (tpt90) REVERT: I 685 MET cc_start: 0.7030 (mpp) cc_final: 0.6676 (mmm) REVERT: I 733 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8741 (m) REVERT: I 750 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7691 (pt) REVERT: I 865 LEU cc_start: 0.8571 (mm) cc_final: 0.8119 (mp) REVERT: J 134 ASP cc_start: 0.5002 (OUTLIER) cc_final: 0.4764 (t0) REVERT: J 147 ILE cc_start: 0.7020 (OUTLIER) cc_final: 0.6703 (tp) REVERT: J 292 VAL cc_start: 0.7861 (m) cc_final: 0.7566 (t) REVERT: J 342 LEU cc_start: 0.9068 (tp) cc_final: 0.8808 (mt) REVERT: J 429 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8010 (mm) REVERT: J 527 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8914 (mt) REVERT: J 631 TYR cc_start: 0.8128 (m-80) cc_final: 0.7791 (m-80) REVERT: J 788 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7519 (mp) REVERT: J 867 GLN cc_start: 0.6149 (mp10) cc_final: 0.5812 (tm-30) REVERT: J 1244 GLN cc_start: 0.8044 (tp-100) cc_final: 0.7592 (mm110) REVERT: K 19 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6244 (tp) REVERT: K 35 LYS cc_start: 0.6997 (mptt) cc_final: 0.6652 (mttt) REVERT: L 51 MET cc_start: 0.0726 (tpp) cc_final: -0.0701 (mtp) REVERT: L 53 ILE cc_start: 0.4231 (mm) cc_final: 0.3984 (mm) REVERT: L 56 MET cc_start: 0.2181 (mmp) cc_final: 0.1373 (tpt) REVERT: L 297 MET cc_start: 0.0460 (ttt) cc_final: 0.0042 (ttm) REVERT: L 320 ILE cc_start: -0.0201 (OUTLIER) cc_final: -0.0496 (tt) REVERT: L 322 MET cc_start: 0.1675 (OUTLIER) cc_final: 0.1435 (ppp) REVERT: L 395 THR cc_start: 0.6346 (p) cc_final: 0.6119 (m) REVERT: L 476 ARG cc_start: 0.5227 (ptt90) cc_final: 0.4844 (ttp-170) REVERT: L 580 PHE cc_start: 0.5076 (OUTLIER) cc_final: 0.4418 (m-10) REVERT: L 595 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5894 (mp) outliers start: 104 outliers final: 78 residues processed: 465 average time/residue: 0.4154 time to fit residues: 316.5941 Evaluate side-chains 457 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 364 time to evaluate : 3.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 173 ASN Chi-restraints excluded: chain I residue 254 ASP Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 851 THR Chi-restraints excluded: chain I residue 916 SER Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1161 LEU Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1198 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 564 VAL Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1050 THR Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1119 ASP Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 322 MET Chi-restraints excluded: chain L residue 513 ASP Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 580 PHE Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 591 GLU Chi-restraints excluded: chain L residue 595 LEU Chi-restraints excluded: chain L residue 613 ASP Chi-restraints excluded: chain M residue 288 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 9.9990 chunk 331 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 286 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 311 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 319 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 HIS ** I 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 330 HIS ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1264 GLN ** J 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.146858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.118981 restraints weight = 61092.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.117278 restraints weight = 88488.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.118420 restraints weight = 83500.365| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 32808 Z= 0.226 Angle : 0.611 12.262 44664 Z= 0.315 Chirality : 0.042 0.192 5130 Planarity : 0.004 0.051 5537 Dihedral : 14.938 144.650 5408 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.28 % Favored : 92.69 % Rotamer: Outliers : 3.23 % Allowed : 27.46 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.33 (0.13), residues: 3845 helix: 0.33 (0.13), residues: 1524 sheet: -1.67 (0.26), residues: 370 loop : -1.73 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 115 HIS 0.009 0.001 HIS J 113 PHE 0.023 0.001 PHE J 172 TYR 0.021 0.001 TYR J 723 ARG 0.007 0.000 ARG J 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7044.35 seconds wall clock time: 127 minutes 58.43 seconds (7678.43 seconds total)