Starting phenix.real_space_refine (version: dev) on Thu Feb 23 23:34:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly9_23589/02_2023/7ly9_23589_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly9_23589/02_2023/7ly9_23589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly9_23589/02_2023/7ly9_23589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly9_23589/02_2023/7ly9_23589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly9_23589/02_2023/7ly9_23589_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly9_23589/02_2023/7ly9_23589_updated.pdb" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.061 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 Process input model Symmetric amino acids flipped Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 100": "OD1" <-> "OD2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 180": "OD1" <-> "OD2" Residue "G PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 267": "OE1" <-> "OE2" Residue "G GLU 466": "OE1" <-> "OE2" Residue "G PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "F PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 584": "OE1" <-> "OE2" Residue "F GLU 654": "OE1" <-> "OE2" Residue "D PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 290": "OE1" <-> "OE2" Residue "D TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 368": "OD1" <-> "OD2" Residue "D TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 50": "OD1" <-> "OD2" Residue "J GLU 588": "OE1" <-> "OE2" Residue "J PHE 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 99": "OD1" <-> "OD2" Residue "K GLU 164": "OE1" <-> "OE2" Residue "K TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 275": "OE1" <-> "OE2" Residue "K GLU 290": "OE1" <-> "OE2" Residue "K GLU 335": "OE1" <-> "OE2" Residue "K PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 477": "OD1" <-> "OD2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 85": "OD1" <-> "OD2" Residue "A ASP 100": "OD1" <-> "OD2" Residue "M ASP 1": "OD1" <-> "OD2" Residue "M TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 96": "OE1" <-> "OE2" Residue "N GLU 584": "OE1" <-> "OE2" Residue "N TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 654": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 21464 Number of models: 1 Model: "" Number of chains: 35 Chain: "L" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 797 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "H" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1023 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3449 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Chain: "B" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "C" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "F" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 899 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain breaks: 1 Chain: "D" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3440 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Chain: "E" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "I" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "J" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 924 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Chain: "K" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3442 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Chain: "A" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "M" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 767 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "N" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 912 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain breaks: 1 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 7 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 7 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 7 Chain: "G" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen chiralities: 16 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 Chain: "M" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 11.80, per 1000 atoms: 0.55 Number of scatterers: 21464 At special positions: 0 Unit cell: (149.07, 139.205, 146.877, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 4299 8.00 N 3572 7.00 C 13467 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.04 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.04 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.04 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS N 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 598 " - pdb=" SG CYS N 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA Q 3 " - " MAN Q 7 " " MAN Q 4 " - " MAN Q 5 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 7 " " MAN U 4 " - " MAN U 5 " " BMA Z 3 " - " MAN Z 7 " " MAN Z 4 " - " MAN Z 5 " ALPHA1-6 " BMA Q 3 " - " MAN Q 4 " " MAN Q 4 " - " MAN Q 6 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 6 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 4 " - " MAN Z 6 " BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " NAG-ASN " NAG C 301 " - " ASN C 72 " " NAG D 601 " - " ASN D 130 " " NAG D 602 " - " ASN D 156 " " NAG D 603 " - " ASN D 230 " " NAG D 604 " - " ASN D 241 " " NAG D 605 " - " ASN D 301 " " NAG D 606 " - " ASN D 362 " " NAG D 607 " - " ASN D 442 " " NAG D 608 " - " ASN D 448 " " NAG D 609 " - " ASN D 393 " " NAG D 610 " - " ASN D 197 " " NAG D 611 " - " ASN D 88 " " NAG D 612 " - " ASN D 234 " " NAG D 613 " - " ASN D 502 " " NAG D 614 " - " ASN D 461 " " NAG D 615 " - " ASN D 356 " " NAG D 616 " - " ASN D 386 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG G 601 " - " ASN G 230 " " NAG G 602 " - " ASN G 241 " " NAG G 603 " - " ASN G 301 " " NAG G 604 " - " ASN G 356 " " NAG G 605 " - " ASN G 362 " " NAG G 606 " - " ASN G 386 " " NAG G 607 " - " ASN G 442 " " NAG G 608 " - " ASN G 448 " " NAG G 609 " - " ASN G 502 " " NAG G 610 " - " ASN G 393 " " NAG G 611 " - " ASN G 197 " " NAG G 612 " - " ASN G 130 " " NAG G 613 " - " ASN G 156 " " NAG G 614 " - " ASN G 234 " " NAG G 615 " - " ASN G 88 " " NAG I 301 " - " ASN I 72 " " NAG J 701 " - " ASN J 637 " " NAG J 702 " - " ASN J 611 " " NAG K 601 " - " ASN K 130 " " NAG K 602 " - " ASN K 156 " " NAG K 603 " - " ASN K 230 " " NAG K 604 " - " ASN K 234 " " NAG K 605 " - " ASN K 241 " " NAG K 606 " - " ASN K 301 " " NAG K 607 " - " ASN K 362 " " NAG K 608 " - " ASN K 386 " " NAG K 609 " - " ASN K 442 " " NAG K 610 " - " ASN K 448 " " NAG K 611 " - " ASN K 393 " " NAG K 612 " - " ASN K 197 " " NAG K 613 " - " ASN K 502 " " NAG K 614 " - " ASN K 88 " " NAG M 301 " - " ASN M 72 " " NAG N 701 " - " ASN N 611 " " NAG N 702 " - " ASN N 637 " " NAG O 1 " - " ASN G 289 " " NAG P 1 " - " ASN G 332 " " NAG Q 1 " - " ASN G 276 " " NAG R 1 " - " ASN G 262 " " NAG S 1 " - " ASN D 289 " " NAG T 1 " - " ASN D 332 " " NAG U 1 " - " ASN D 276 " " NAG V 1 " - " ASN D 262 " " NAG W 1 " - " ASN K 262 " " NAG X 1 " - " ASN K 289 " " NAG Y 1 " - " ASN K 332 " " NAG Z 1 " - " ASN K 276 " Time building additional restraints: 9.55 Conformation dependent library (CDL) restraints added in 2.9 seconds 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 50 sheets defined 15.8% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'L' and resid 28 through 30 No H-bonds generated for 'chain 'L' and resid 28 through 30' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'H' and resid 61 through 63 No H-bonds generated for 'chain 'H' and resid 61 through 63' Processing helix chain 'G' and resid 95 through 97 No H-bonds generated for 'chain 'G' and resid 95 through 97' Processing helix chain 'G' and resid 100 through 115 Processing helix chain 'G' and resid 335 through 353 removed outlier: 3.716A pdb=" N GLU G 351 " --> pdb=" O GLU G 347 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N HIS G 352 " --> pdb=" O LYS G 348 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE G 353 " --> pdb=" O LEU G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 372 No H-bonds generated for 'chain 'G' and resid 369 through 372' Processing helix chain 'G' and resid 389 through 391 No H-bonds generated for 'chain 'G' and resid 389 through 391' Processing helix chain 'G' and resid 475 through 480 removed outlier: 3.553A pdb=" N ARG G 480 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'F' and resid 516 through 523 removed outlier: 3.806A pdb=" N PHE F 522 " --> pdb=" O VAL F 518 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU F 523 " --> pdb=" O PHE F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 535 removed outlier: 3.994A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 6.262A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR F 586 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU F 587 " --> pdb=" O ILE F 583 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 625 Processing helix chain 'F' and resid 628 through 656 removed outlier: 3.666A pdb=" N ARG F 633 " --> pdb=" O MET F 629 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN F 637 " --> pdb=" O ARG F 633 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N TYR F 638 " --> pdb=" O GLU F 634 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASP F 640 " --> pdb=" O GLY F 636 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N THR F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL F 648 " --> pdb=" O LYS F 644 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 99 through 118 removed outlier: 3.556A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) Proline residue: D 118 - end of helix Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 335 through 353 removed outlier: 3.553A pdb=" N GLN D 343 " --> pdb=" O GLU D 339 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU D 351 " --> pdb=" O GLU D 347 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 480 removed outlier: 3.593A pdb=" N ARG D 480 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 86 No H-bonds generated for 'chain 'E' and resid 84 through 86' Processing helix chain 'J' and resid 516 through 523 removed outlier: 3.515A pdb=" N PHE J 522 " --> pdb=" O VAL J 518 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU J 523 " --> pdb=" O PHE J 519 " (cutoff:3.500A) Processing helix chain 'J' and resid 530 through 535 removed outlier: 3.518A pdb=" N SER J 534 " --> pdb=" O MET J 530 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN J 535 " --> pdb=" O GLY J 531 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 530 through 535' Processing helix chain 'J' and resid 570 through 596 removed outlier: 6.396A pdb=" N GLN J 575 " --> pdb=" O TRP J 571 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 625 Processing helix chain 'J' and resid 628 through 659 removed outlier: 3.730A pdb=" N ASP J 632 " --> pdb=" O TRP J 628 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG J 633 " --> pdb=" O MET J 629 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ASN J 637 " --> pdb=" O ARG J 633 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N TYR J 638 " --> pdb=" O GLU J 634 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASP J 640 " --> pdb=" O GLY J 636 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N THR J 641 " --> pdb=" O ASN J 637 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL J 648 " --> pdb=" O LYS J 644 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS J 658 " --> pdb=" O GLU J 654 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 116 Processing helix chain 'K' and resid 335 through 353 removed outlier: 3.688A pdb=" N LYS K 348 " --> pdb=" O ARG K 344 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU K 351 " --> pdb=" O GLU K 347 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N HIS K 352 " --> pdb=" O LYS K 348 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE K 353 " --> pdb=" O LEU K 349 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 372 No H-bonds generated for 'chain 'K' and resid 369 through 372' Processing helix chain 'K' and resid 389 through 391 No H-bonds generated for 'chain 'K' and resid 389 through 391' Processing helix chain 'K' and resid 476 through 481 removed outlier: 3.723A pdb=" N SER K 481 " --> pdb=" O ASP K 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'N' and resid 517 through 523 removed outlier: 3.828A pdb=" N LEU N 523 " --> pdb=" O PHE N 519 " (cutoff:3.500A) Processing helix chain 'N' and resid 530 through 535 Processing helix chain 'N' and resid 570 through 596 removed outlier: 6.583A pdb=" N GLN N 575 " --> pdb=" O TRP N 571 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU N 576 " --> pdb=" O GLY N 572 " (cutoff:3.500A) Processing helix chain 'N' and resid 628 through 658 removed outlier: 3.610A pdb=" N ASP N 632 " --> pdb=" O TRP N 628 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG N 633 " --> pdb=" O MET N 629 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU N 634 " --> pdb=" O GLN N 630 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ASN N 637 " --> pdb=" O ARG N 633 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N TYR N 638 " --> pdb=" O GLU N 634 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ASP N 640 " --> pdb=" O GLY N 636 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N THR N 641 " --> pdb=" O ASN N 637 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN N 650 " --> pdb=" O LEU N 646 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE N 651 " --> pdb=" O GLU N 647 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'L' and resid 22 through 24 removed outlier: 3.632A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'L' and resid 34 through 38 removed outlier: 3.540A pdb=" N ASP L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL L 90 " --> pdb=" O VAL L 97 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL L 97 " --> pdb=" O VAL L 90 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.191A pdb=" N SER H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP H 72 " --> pdb=" O SER H 77 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR H 79 " --> pdb=" O SER H 70 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 89 through 95 removed outlier: 3.528A pdb=" N PHE H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA H 93 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N THR H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 35 through 40 removed outlier: 3.586A pdb=" N THR G 499 " --> pdb=" O TRP G 35 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.508A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 53 through 55 removed outlier: 3.512A pdb=" N PHE G 53 " --> pdb=" O CYS G 218 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.538A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE G 93 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 154 through 162 Processing sheet with id= J, first strand: chain 'G' and resid 181 through 183 Processing sheet with id= K, first strand: chain 'G' and resid 200 through 203 removed outlier: 3.873A pdb=" N THR G 202 " --> pdb=" O ALA G 433 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 271 through 274 Processing sheet with id= M, first strand: chain 'G' and resid 292 through 298 removed outlier: 3.730A pdb=" N CYS G 445 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG G 298 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 332 through 334 Processing sheet with id= O, first strand: chain 'G' and resid 374 through 378 removed outlier: 3.861A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE G 383 " --> pdb=" O PHE G 376 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR G 384 " --> pdb=" O ARG G 419 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG G 419 " --> pdb=" O TYR G 384 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 454 through 456 Processing sheet with id= Q, first strand: chain 'G' and resid 304 through 312 removed outlier: 3.657A pdb=" N ILE G 309 " --> pdb=" O GLN G 315 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.579A pdb=" N GLU B 23 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL B 18 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU B 82 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 20 " --> pdb=" O MET B 80 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR B 70 " --> pdb=" O TYR B 79 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 107 through 109 removed outlier: 3.505A pdb=" N HIS B 35 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B 33 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 34 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 85 through 89 removed outlier: 3.743A pdb=" N PHE C 87 " --> pdb=" O TYR C 36 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE C 48 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN C 37 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU C 46 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 36 through 40 Processing sheet with id= V, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.664A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 91 through 94 removed outlier: 3.510A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE D 93 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY D 237 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 154 through 161 removed outlier: 3.743A pdb=" N ARG D 170 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= Z, first strand: chain 'D' and resid 270 through 274 Processing sheet with id= AA, first strand: chain 'D' and resid 443 through 445 removed outlier: 4.060A pdb=" N ILE D 443 " --> pdb=" O ARG D 298 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR D 295 " --> pdb=" O ASN D 332 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN D 332 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR D 297 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N HIS D 330 " --> pdb=" O THR D 297 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 359 through 362 removed outlier: 6.298A pdb=" N GLU D 466 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ASN D 362 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N PHE D 468 " --> pdb=" O ASN D 362 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 374 through 378 removed outlier: 3.693A pdb=" N PHE D 376 " --> pdb=" O PHE D 383 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR D 384 " --> pdb=" O ARG D 419 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG D 419 " --> pdb=" O TYR D 384 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 305 through 312 removed outlier: 3.773A pdb=" N LYS D 305 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 18 through 24 removed outlier: 3.857A pdb=" N VAL E 18 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU E 82 " --> pdb=" O VAL E 18 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 107 through 109 removed outlier: 3.525A pdb=" N TYR E 90 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP E 37 " --> pdb=" O PHE E 91 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE E 34 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 18 through 22 removed outlier: 3.882A pdb=" N SER I 63 " --> pdb=" O THR I 74 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 87 through 89 removed outlier: 3.625A pdb=" N TRP I 35 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE I 48 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'K' and resid 45 through 47 Processing sheet with id= AJ, first strand: chain 'K' and resid 53 through 55 removed outlier: 3.599A pdb=" N PHE K 53 " --> pdb=" O CYS K 218 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'K' and resid 91 through 94 removed outlier: 4.173A pdb=" N PHE K 93 " --> pdb=" O GLY K 237 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY K 237 " --> pdb=" O PHE K 93 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'K' and resid 154 through 161 removed outlier: 4.062A pdb=" N ALA K 161 " --> pdb=" O ARG K 170 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG K 170 " --> pdb=" O ALA K 161 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'K' and resid 181 through 183 Processing sheet with id= AN, first strand: chain 'K' and resid 200 through 203 removed outlier: 3.602A pdb=" N ALA K 433 " --> pdb=" O VAL K 200 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR K 202 " --> pdb=" O ALA K 433 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'K' and resid 271 through 273 Processing sheet with id= AP, first strand: chain 'K' and resid 292 through 298 removed outlier: 3.681A pdb=" N VAL K 292 " --> pdb=" O ILE K 449 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS K 445 " --> pdb=" O CYS K 296 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG K 298 " --> pdb=" O ILE K 443 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE K 443 " --> pdb=" O ARG K 298 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'K' and resid 304 through 308 Processing sheet with id= AR, first strand: chain 'K' and resid 332 through 334 Processing sheet with id= AS, first strand: chain 'K' and resid 360 through 362 Processing sheet with id= AT, first strand: chain 'K' and resid 374 through 378 removed outlier: 3.750A pdb=" N PHE K 376 " --> pdb=" O PHE K 383 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE K 382 " --> pdb=" O LYS K 421 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS K 421 " --> pdb=" O PHE K 382 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR K 384 " --> pdb=" O ARG K 419 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG K 419 " --> pdb=" O TYR K 384 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'A' and resid 4 through 6 removed outlier: 4.103A pdb=" N VAL A 18 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A 82 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 77 " --> pdb=" O HIS A 71A" (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP A 81 " --> pdb=" O SER A 68 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'A' and resid 107 through 109 removed outlier: 3.520A pdb=" N THR A 107 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 90 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 34 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA A 40 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 45 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'M' and resid 4 through 6 removed outlier: 3.525A pdb=" N ILE M 21 " --> pdb=" O LEU M 73 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TRP M 67 " --> pdb=" O GLU M 70 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASN M 72 " --> pdb=" O ARG M 65 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG M 65 " --> pdb=" O ASN M 72 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER M 63 " --> pdb=" O THR M 74 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'M' and resid 85 through 89 removed outlier: 3.861A pdb=" N ILE M 48 " --> pdb=" O TRP M 35 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN M 37 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU M 46 " --> pdb=" O GLN M 37 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.77 Time building geometry restraints manager: 10.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3520 1.32 - 1.45: 6391 1.45 - 1.58: 11851 1.58 - 1.70: 2 1.70 - 1.83: 166 Bond restraints: 21930 Sorted by residual: bond pdb=" OH TYS H 100A" pdb=" S TYS H 100A" ideal model delta sigma weight residual 1.679 1.564 0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" CA TYR C 91 " pdb=" C TYR C 91 " ideal model delta sigma weight residual 1.523 1.587 -0.064 1.34e-02 5.57e+03 2.29e+01 bond pdb=" OH TYS H 100C" pdb=" S TYS H 100C" ideal model delta sigma weight residual 1.679 1.600 0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" N THR D 358 " pdb=" CA THR D 358 " ideal model delta sigma weight residual 1.456 1.501 -0.045 1.22e-02 6.72e+03 1.37e+01 bond pdb=" N GLU G 190 " pdb=" CA GLU G 190 " ideal model delta sigma weight residual 1.455 1.499 -0.044 1.25e-02 6.40e+03 1.23e+01 ... (remaining 21925 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.31: 556 106.31 - 113.27: 12357 113.27 - 120.23: 7208 120.23 - 127.19: 9358 127.19 - 134.16: 307 Bond angle restraints: 29786 Sorted by residual: angle pdb=" C ASN D 262 " pdb=" CA ASN D 262 " pdb=" CB ASN D 262 " ideal model delta sigma weight residual 115.89 105.59 10.30 1.32e+00 5.74e-01 6.09e+01 angle pdb=" CA TYR C 91 " pdb=" C TYR C 91 " pdb=" O TYR C 91 " ideal model delta sigma weight residual 120.51 111.88 8.63 1.43e+00 4.89e-01 3.64e+01 angle pdb=" CA TYR C 91 " pdb=" C TYR C 91 " pdb=" N GLU C 96 " ideal model delta sigma weight residual 116.84 125.45 -8.61 1.71e+00 3.42e-01 2.54e+01 angle pdb=" CA PRO G 214 " pdb=" C PRO G 214 " pdb=" O PRO G 214 " ideal model delta sigma weight residual 121.36 115.89 5.47 1.13e+00 7.83e-01 2.34e+01 angle pdb=" CA ASN D 262 " pdb=" CB ASN D 262 " pdb=" CG ASN D 262 " ideal model delta sigma weight residual 112.60 117.36 -4.76 1.00e+00 1.00e+00 2.27e+01 ... (remaining 29781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11601 17.95 - 35.90: 1039 35.90 - 53.85: 232 53.85 - 71.80: 26 71.80 - 89.75: 21 Dihedral angle restraints: 12919 sinusoidal: 5616 harmonic: 7303 Sorted by residual: dihedral pdb=" CB CYS F 598 " pdb=" SG CYS F 598 " pdb=" SG CYS F 604 " pdb=" CB CYS F 604 " ideal model delta sinusoidal sigma weight residual 93.00 166.44 -73.44 1 1.00e+01 1.00e-02 6.86e+01 dihedral pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " pdb=" CB CYS D 196 " ideal model delta sinusoidal sigma weight residual -86.00 -141.05 55.05 1 1.00e+01 1.00e-02 4.10e+01 dihedral pdb=" CB CYS D 218 " pdb=" SG CYS D 218 " pdb=" SG CYS D 247 " pdb=" CB CYS D 247 " ideal model delta sinusoidal sigma weight residual -86.00 -136.25 50.25 1 1.00e+01 1.00e-02 3.46e+01 ... (remaining 12916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 3478 0.134 - 0.267: 50 0.267 - 0.401: 8 0.401 - 0.535: 1 0.535 - 0.669: 1 Chirality restraints: 3538 Sorted by residual: chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN D 262 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" CA THR G 209 " pdb=" N THR G 209 " pdb=" C THR G 209 " pdb=" CB THR G 209 " both_signs ideal model delta sigma weight residual False 2.53 2.94 -0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CA LEU D 261 " pdb=" N LEU D 261 " pdb=" C LEU D 261 " pdb=" CB LEU D 261 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 3535 not shown) Planarity restraints: 3752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 262 " 0.041 2.00e-02 2.50e+03 4.13e-02 2.13e+01 pdb=" CG ASN D 262 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN D 262 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN D 262 " -0.062 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 252 " 0.061 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO D 253 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO D 253 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 253 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 208 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C VAL G 208 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL G 208 " 0.023 2.00e-02 2.50e+03 pdb=" N THR G 209 " 0.020 2.00e-02 2.50e+03 ... (remaining 3749 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 237 2.58 - 3.16: 18124 3.16 - 3.74: 29919 3.74 - 4.32: 42067 4.32 - 4.90: 70710 Nonbonded interactions: 161057 Sorted by model distance: nonbonded pdb=" OD2 ASP G 457 " pdb=" OG1 THR G 467 " model vdw 2.003 2.440 nonbonded pdb=" O THR G 209 " pdb=" OG1 THR G 209 " model vdw 2.160 2.440 nonbonded pdb=" O PRO C 8 " pdb=" OG SER C 9 " model vdw 2.222 2.440 nonbonded pdb=" NH2 ARG I 66 " pdb=" O7 NAG U 2 " model vdw 2.233 2.520 nonbonded pdb=" O SER N 612 " pdb=" ND2 ASN N 616 " model vdw 2.245 2.520 ... (remaining 161052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 1 through 104 or resid 301)) selection = (chain 'I' and (resid 1 through 104 or resid 301)) selection = chain 'M' } ncs_group { reference = (chain 'D' and (resid 33 through 503 or resid 603 through 615)) selection = (chain 'G' and (resid 33 through 397 or resid 410 through 503 or resid 603 throu \ gh 615)) selection = (chain 'K' and (resid 33 through 397 or resid 410 through 503 or resid 601 throu \ gh 613)) } ncs_group { reference = (chain 'F' and (resid 516 through 657 or resid 701 through 702)) selection = (chain 'J' and (resid 516 through 657 or resid 701 through 702)) selection = (chain 'N' and (resid 516 through 657 or resid 701 through 702)) } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = chain 'Q' selection = chain 'U' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 13467 2.51 5 N 3572 2.21 5 O 4299 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.730 Check model and map are aligned: 0.330 Process input model: 55.730 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Set scattering table: 0.230 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.115 21930 Z= 0.212 Angle : 0.597 10.301 29786 Z= 0.346 Chirality : 0.050 0.669 3538 Planarity : 0.003 0.094 3686 Dihedral : 13.910 89.754 8103 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.78 % Favored : 94.18 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2475 helix: 1.78 (0.32), residues: 318 sheet: 0.17 (0.22), residues: 609 loop : -0.71 (0.16), residues: 1548 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 194 time to evaluate : 2.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 4 residues processed: 210 average time/residue: 0.4166 time to fit residues: 127.4733 Evaluate side-chains 101 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 2.639 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2020 time to fit residues: 4.9355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 208 optimal weight: 0.0570 chunk 187 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 117 optimal weight: 0.0010 chunk 144 optimal weight: 8.9990 chunk 224 optimal weight: 3.9990 overall best weight: 2.4110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 10 ASN G 105 HIS G 377 ASN B 6 GLN F 653 GLN D 287 HIS D 330 HIS ** K 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 377 ASN ** K 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 653 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 21930 Z= 0.297 Angle : 0.635 8.004 29786 Z= 0.338 Chirality : 0.046 0.331 3538 Planarity : 0.005 0.100 3686 Dihedral : 5.177 44.739 3385 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.17), residues: 2475 helix: 1.41 (0.29), residues: 327 sheet: 0.03 (0.21), residues: 625 loop : -0.91 (0.16), residues: 1523 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 8 residues processed: 115 average time/residue: 0.3467 time to fit residues: 63.8159 Evaluate side-chains 94 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 2.628 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1990 time to fit residues: 6.3474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 124 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 224 optimal weight: 2.9990 chunk 242 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 222 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 180 optimal weight: 0.0050 overall best weight: 1.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 203 GLN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 HIS ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 195 ASN K 425 ASN A 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 21930 Z= 0.232 Angle : 0.562 8.605 29786 Z= 0.297 Chirality : 0.044 0.346 3538 Planarity : 0.004 0.064 3686 Dihedral : 5.106 43.115 3385 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.17), residues: 2475 helix: 1.61 (0.29), residues: 324 sheet: -0.01 (0.20), residues: 648 loop : -0.96 (0.16), residues: 1503 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 2.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 6 residues processed: 103 average time/residue: 0.3268 time to fit residues: 55.7566 Evaluate side-chains 85 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 2.747 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2090 time to fit residues: 5.8838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 222 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 chunk 116 optimal weight: 0.0370 chunk 24 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 225 optimal weight: 0.9980 chunk 238 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82AASN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 21930 Z= 0.198 Angle : 0.539 8.510 29786 Z= 0.284 Chirality : 0.044 0.331 3538 Planarity : 0.003 0.041 3686 Dihedral : 5.077 43.272 3385 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.33 % Favored : 94.63 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.17), residues: 2475 helix: 1.74 (0.29), residues: 326 sheet: -0.01 (0.20), residues: 658 loop : -0.92 (0.16), residues: 1491 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 2.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 98 average time/residue: 0.3402 time to fit residues: 54.5995 Evaluate side-chains 91 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 2.590 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1966 time to fit residues: 7.5023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 198 optimal weight: 0.0870 chunk 135 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 165 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 GLN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 591 GLN N 653 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 21930 Z= 0.148 Angle : 0.516 8.828 29786 Z= 0.270 Chirality : 0.043 0.323 3538 Planarity : 0.003 0.044 3686 Dihedral : 4.991 43.127 3385 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.09 % Favored : 94.87 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.17), residues: 2475 helix: 1.88 (0.29), residues: 323 sheet: 0.15 (0.21), residues: 642 loop : -0.93 (0.16), residues: 1510 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 2.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 13 residues processed: 111 average time/residue: 0.3361 time to fit residues: 61.4143 Evaluate side-chains 96 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 2.665 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.2441 time to fit residues: 8.8610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 80 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 47 optimal weight: 0.0050 chunk 140 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 238 optimal weight: 9.9990 chunk 198 optimal weight: 0.0170 chunk 110 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 21930 Z= 0.301 Angle : 0.592 10.780 29786 Z= 0.310 Chirality : 0.044 0.315 3538 Planarity : 0.004 0.035 3686 Dihedral : 5.242 44.605 3385 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.17), residues: 2475 helix: 2.13 (0.29), residues: 318 sheet: 0.06 (0.21), residues: 656 loop : -0.99 (0.16), residues: 1501 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 83 time to evaluate : 2.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 104 average time/residue: 0.3176 time to fit residues: 55.4709 Evaluate side-chains 93 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 2.574 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.1967 time to fit residues: 8.8345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 230 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 136 optimal weight: 2.9990 chunk 174 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 201 optimal weight: 0.8980 chunk 133 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 21930 Z= 0.231 Angle : 0.555 11.316 29786 Z= 0.290 Chirality : 0.044 0.305 3538 Planarity : 0.003 0.036 3686 Dihedral : 5.226 44.053 3385 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.58 % Favored : 94.38 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.17), residues: 2475 helix: 2.15 (0.29), residues: 318 sheet: -0.06 (0.20), residues: 712 loop : -1.00 (0.16), residues: 1445 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 94 average time/residue: 0.3379 time to fit residues: 52.6628 Evaluate side-chains 87 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 2.638 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.2012 time to fit residues: 7.0933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 147 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 187 optimal weight: 3.9990 chunk 216 optimal weight: 8.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 66 ASN B 108 GLN F 616 ASN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 21930 Z= 0.234 Angle : 0.556 11.831 29786 Z= 0.290 Chirality : 0.044 0.349 3538 Planarity : 0.003 0.036 3686 Dihedral : 5.246 43.960 3385 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.82 % Favored : 94.14 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.17), residues: 2475 helix: 2.13 (0.29), residues: 315 sheet: -0.19 (0.19), residues: 738 loop : -1.04 (0.16), residues: 1422 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 90 average time/residue: 0.3364 time to fit residues: 50.6060 Evaluate side-chains 81 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 2.711 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1937 time to fit residues: 4.3030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 228 optimal weight: 8.9990 chunk 208 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 174 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 209 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 234 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 21930 Z= 0.184 Angle : 0.546 12.743 29786 Z= 0.283 Chirality : 0.044 0.335 3538 Planarity : 0.003 0.037 3686 Dihedral : 5.200 43.635 3385 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.70 % Favored : 94.26 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.17), residues: 2475 helix: 2.19 (0.30), residues: 315 sheet: -0.14 (0.20), residues: 722 loop : -1.00 (0.16), residues: 1438 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 2.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 85 average time/residue: 0.3259 time to fit residues: 46.7548 Evaluate side-chains 81 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 2.594 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1930 time to fit residues: 4.7524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 143 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 246 optimal weight: 7.9990 chunk 226 optimal weight: 0.9980 chunk 195 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 208 optimal weight: 0.0470 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 21930 Z= 0.188 Angle : 0.552 13.082 29786 Z= 0.283 Chirality : 0.043 0.329 3538 Planarity : 0.003 0.039 3686 Dihedral : 5.172 43.496 3385 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.86 % Favored : 94.10 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.17), residues: 2475 helix: 2.20 (0.30), residues: 315 sheet: -0.10 (0.20), residues: 716 loop : -1.03 (0.16), residues: 1444 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 85 average time/residue: 0.3331 time to fit residues: 47.7463 Evaluate side-chains 82 residues out of total 2223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 2.645 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1916 time to fit residues: 4.1337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 60 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 196 optimal weight: 5.9990 chunk 82 optimal weight: 0.2980 chunk 201 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 172 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 ASN F 656 ASN ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 GLN ** M 24 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 = 0.2953 r_free = 0.2953 target = 0.033038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.026321 restraints weight = 191095.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.027173 restraints weight = 102646.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.027757 restraints weight = 68919.342| |-----------------------------------------------------------------------------| r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 21930 Z= 0.404 Angle : 0.673 12.586 29786 Z= 0.349 Chirality : 0.045 0.328 3538 Planarity : 0.004 0.050 3686 Dihedral : 5.610 44.340 3385 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.35 % Favored : 92.61 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.17), residues: 2475 helix: 1.86 (0.29), residues: 321 sheet: -0.29 (0.19), residues: 731 loop : -1.18 (0.16), residues: 1423 =============================================================================== Job complete usr+sys time: 2961.57 seconds wall clock time: 56 minutes 16.04 seconds (3376.04 seconds total)