Starting phenix.real_space_refine (version: dev) on Wed Feb 22 17:03:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo6_23462/02_2023/7lo6_23462_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo6_23462/02_2023/7lo6_23462.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo6_23462/02_2023/7lo6_23462_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo6_23462/02_2023/7lo6_23462_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo6_23462/02_2023/7lo6_23462_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo6_23462/02_2023/7lo6_23462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo6_23462/02_2023/7lo6_23462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo6_23462/02_2023/7lo6_23462_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo6_23462/02_2023/7lo6_23462_updated.pdb" } resolution = 3.9 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= 0.000 sd= 0.002 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 "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 419": "NH1" <-> "NH2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 444": "NH1" <-> "NH2" Residue "A ASP 474": "OD1" <-> "OD2" Residue "B TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 589": "OD1" <-> "OD2" Residue "B GLU 647": "OE1" <-> "OE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "C ARG 419": "NH1" <-> "NH2" Residue "C TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 444": "NH1" <-> "NH2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C ASP 474": "OD1" <-> "OD2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 542": "NH1" <-> "NH2" Residue "D GLU 584": "OE1" <-> "OE2" Residue "D ARG 585": "NH1" <-> "NH2" Residue "D TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E GLU 268": "OE1" <-> "OE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 419": "NH1" <-> "NH2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 584": "OE1" <-> "OE2" Residue "F TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 648": "OE1" <-> "OE2" Residue "G ARG 18": "NH1" <-> "NH2" Residue "G ARG 24": "NH1" <-> "NH2" Residue "G PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 97": "NH1" <-> "NH2" Residue "H GLU 1": "OE1" <-> "OE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 18": "NH1" <-> "NH2" Residue "I ARG 24": "NH1" <-> "NH2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 97": "NH1" <-> "NH2" Residue "J GLU 10": "OE1" <-> "OE2" Residue "J PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 90": "OD1" <-> "OD2" Residue "J TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K ARG 24": "NH1" <-> "NH2" Residue "K TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 97": "NH1" <-> "NH2" Residue "K TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 1": "OE1" <-> "OE2" Residue "L GLU 46": "OE1" <-> "OE2" Residue "L TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 90": "OD1" <-> "OD2" Residue "L PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 18006 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2840 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 341} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1026 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2848 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 342} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1049 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2862 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 21, 'TRANS': 343} Chain breaks: 4 Chain: "F" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 996 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "I" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 850 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 996 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "K" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 996 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "M" 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: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 6 Chain: "Q" 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: "R" 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: "S" 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: "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: 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: "V" 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: "A" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 143 Unusual residues: {'5VG': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 143 Unusual residues: {'5VG': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "D" 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: "E" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 143 Unusual residues: {'5VG': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 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 Time building chain proxies: 9.92, per 1000 atoms: 0.55 Number of scatterers: 18006 At special positions: 0 Unit cell: (149.04, 139.104, 156.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 3 17.00 S 108 16.00 F 3 9.00 O 3542 8.00 N 3048 7.00 C 11302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 385 " distance=2.07 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.02 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " 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=4, symmetry=0 Links applied ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN S 4 " - " MAN S 5 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA S 3 " - " MAN S 4 " " MAN S 6 " - " MAN S 7 " ALPHA1-6 " MAN N 4 " - " MAN N 5 " " BMA P 3 " - " MAN P 6 " " BMA S 3 " - " MAN S 6 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 602 " - " ASN A 276 " " NAG A 603 " - " ASN A 295 " " NAG A 604 " - " ASN A 332 " " NAG A 605 " - " ASN A 339 " " NAG A 606 " - " ASN A 363 " " NAG A 607 " - " ASN A 392 " " NAG A 608 " - " ASN A 448 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 295 " " NAG C 603 " - " ASN C 332 " " NAG C 604 " - " ASN C 339 " " NAG C 605 " - " ASN C 355 " " NAG C 606 " - " ASN C 363 " " NAG C 607 " - " ASN C 392 " " NAG C 608 " - " ASN C 448 " " NAG D 701 " - " ASN D 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 295 " " NAG E 604 " - " ASN E 332 " " NAG E 605 " - " ASN E 355 " " NAG E 606 " - " ASN E 363 " " NAG E 607 " - " ASN E 392 " " NAG E 608 " - " ASN E 448 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG M 1 " - " ASN A 386 " " NAG N 1 " - " ASN A 262 " " NAG O 1 " - " ASN C 234 " " NAG P 1 " - " ASN C 262 " " NAG Q 1 " - " ASN C 276 " " NAG R 1 " - " ASN C 386 " " NAG S 1 " - " ASN E 262 " " NAG T 1 " - " ASN E 276 " " NAG U 1 " - " ASN E 339 " " NAG V 1 " - " ASN E 386 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.52 Conformation dependent library (CDL) restraints added in 2.5 seconds 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4068 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 35 sheets defined 17.4% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 removed outlier: 4.425A pdb=" N ALA A 70 " --> pdb=" O HIS A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 115 removed outlier: 3.511A pdb=" N LEU A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLN A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 352 removed outlier: 4.334A pdb=" N GLY A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 478 Processing helix chain 'B' and resid 515 through 523 removed outlier: 3.928A pdb=" N PHE B 519 " --> pdb=" O GLY B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 543 removed outlier: 4.214A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 565 No H-bonds generated for 'chain 'B' and resid 563 through 565' Processing helix chain 'B' and resid 569 through 596 removed outlier: 4.066A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 595 " --> pdb=" O GLN B 591 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 623 No H-bonds generated for 'chain 'B' and resid 620 through 623' Processing helix chain 'B' and resid 628 through 635 Processing helix chain 'B' and resid 639 through 655 removed outlier: 3.600A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 Processing helix chain 'C' and resid 100 through 115 Processing helix chain 'C' and resid 336 through 352 removed outlier: 3.917A pdb=" N GLY C 343 " --> pdb=" O ASN C 339 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 478 removed outlier: 3.686A pdb=" N ASN C 478 " --> pdb=" O MET C 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 475 through 478' Processing helix chain 'C' and resid 480 through 482 No H-bonds generated for 'chain 'C' and resid 480 through 482' Processing helix chain 'D' and resid 515 through 525 removed outlier: 3.683A pdb=" N PHE D 519 " --> pdb=" O GLY D 516 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA D 525 " --> pdb=" O PHE D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 545 removed outlier: 4.749A pdb=" N THR D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N VAL D 539 " --> pdb=" O MET D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 595 removed outlier: 3.985A pdb=" N LEU D 568 " --> pdb=" O HIS D 564 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N TRP D 571 " --> pdb=" O LYS D 567 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE D 573 " --> pdb=" O THR D 569 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ALA D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG D 579 " --> pdb=" O GLN D 575 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL D 580 " --> pdb=" O LEU D 576 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG D 585 " --> pdb=" O LEU D 581 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY D 594 " --> pdb=" O GLN D 590 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE D 595 " --> pdb=" O GLN D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 635 Processing helix chain 'D' and resid 639 through 654 removed outlier: 3.642A pdb=" N GLU D 654 " --> pdb=" O GLN D 650 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 73 removed outlier: 3.924A pdb=" N HIS E 72 " --> pdb=" O VAL E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 114 removed outlier: 3.709A pdb=" N ASP E 107 " --> pdb=" O GLN E 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 341 Processing helix chain 'E' and resid 343 through 352 removed outlier: 3.623A pdb=" N GLN E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 526 removed outlier: 4.088A pdb=" N ALA F 525 " --> pdb=" O PHE F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 540 removed outlier: 3.664A pdb=" N THR F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL F 539 " --> pdb=" O MET F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 573 through 595 removed outlier: 4.418A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU F 584 " --> pdb=" O VAL F 580 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG F 588 " --> pdb=" O GLU F 584 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN F 591 " --> pdb=" O LEU F 587 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY F 594 " --> pdb=" O GLN F 590 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE F 595 " --> pdb=" O GLN F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 628 through 635 Processing helix chain 'F' and resid 639 through 657 removed outlier: 3.851A pdb=" N GLU F 654 " --> pdb=" O GLN F 650 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS F 655 " --> pdb=" O ASN F 651 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU F 657 " --> pdb=" O GLN F 653 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 82 No H-bonds generated for 'chain 'G' and resid 80 through 82' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing helix chain 'L' and resid 88 through 90 No H-bonds generated for 'chain 'L' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 39 Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.766A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 83 through 85 Processing sheet with id= E, first strand: chain 'A' and resid 92 through 94 removed outlier: 4.041A pdb=" N PHE A 93 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.713A pdb=" N VAL A 120 " --> pdb=" O MET A 434 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 424 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 444 through 449 removed outlier: 8.256A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.528A pdb=" N CYS A 385 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 35 through 39 Processing sheet with id= J, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.628A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= L, first strand: chain 'C' and resid 91 through 94 removed outlier: 4.576A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS C 239 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 292 through 294 removed outlier: 3.824A pdb=" N VAL C 292 " --> pdb=" O ILE C 449 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 295 through 297 removed outlier: 3.592A pdb=" N ASN C 332 " --> pdb=" O ASN C 295 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 358 through 361 Processing sheet with id= P, first strand: chain 'C' and resid 374 through 378 Processing sheet with id= Q, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= R, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= S, first strand: chain 'E' and resid 91 through 93 removed outlier: 4.030A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 197 through 202 removed outlier: 3.898A pdb=" N SER E 199 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR E 123 " --> pdb=" O SER E 199 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL E 120 " --> pdb=" O MET E 434 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 443 through 447 removed outlier: 3.716A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 465 through 469 removed outlier: 6.811A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 4 through 7 Processing sheet with id= X, first strand: chain 'G' and resid 85 through 90 removed outlier: 6.010A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.579A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.541A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 5 through 7 Processing sheet with id= AB, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.852A pdb=" N ARG I 105 " --> pdb=" O LEU I 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'I' and resid 85 through 89 removed outlier: 3.673A pdb=" N ILE I 48 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.733A pdb=" N THR J 78 " --> pdb=" O ASP J 73 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP J 73 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.929A pdb=" N VAL J 99 " --> pdb=" O SER J 33 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 84 through 86 removed outlier: 3.508A pdb=" N GLN K 38 " --> pdb=" O VAL K 85 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LYS K 39 " --> pdb=" O PRO K 44 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'K' and resid 65 through 67 Processing sheet with id= AH, first strand: chain 'L' and resid 17 through 20 Processing sheet with id= AI, first strand: chain 'L' and resid 92 through 100 removed outlier: 3.952A pdb=" N PHE L 34 " --> pdb=" O ILE L 51 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP L 36 " --> pdb=" O GLY L 49 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TRP L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ALA L 40 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU L 45 " --> pdb=" O ALA L 40 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1140 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: 5.01 Time building geometry restraints manager: 8.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2896 1.30 - 1.44: 5184 1.44 - 1.58: 10159 1.58 - 1.71: 0 1.71 - 1.85: 147 Bond restraints: 18386 Sorted by residual: bond pdb=" CA TRP E 96 " pdb=" C TRP E 96 " ideal model delta sigma weight residual 1.523 1.447 0.076 1.80e-02 3.09e+03 1.78e+01 bond pdb=" C CYS E 239 " pdb=" N PRO E 240 " ideal model delta sigma weight residual 1.334 1.303 0.031 8.40e-03 1.42e+04 1.35e+01 bond pdb=" N ILE C 449 " pdb=" CA ILE C 449 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.25e-02 6.40e+03 8.73e+00 bond pdb=" CA THR E 71 " pdb=" C THR E 71 " ideal model delta sigma weight residual 1.518 1.402 0.116 4.01e-02 6.22e+02 8.41e+00 bond pdb=" CA ARG E 480 " pdb=" C ARG E 480 " ideal model delta sigma weight residual 1.518 1.403 0.115 4.01e-02 6.22e+02 8.23e+00 ... (remaining 18381 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.92: 392 105.92 - 112.97: 10616 112.97 - 120.02: 5798 120.02 - 127.07: 7906 127.07 - 134.12: 265 Bond angle restraints: 24977 Sorted by residual: angle pdb=" N ALA D 561 " pdb=" CA ALA D 561 " pdb=" C ALA D 561 " ideal model delta sigma weight residual 112.45 119.92 -7.47 1.39e+00 5.18e-01 2.89e+01 angle pdb=" C2 NAG C 604 " pdb=" N2 NAG C 604 " pdb=" C7 NAG C 604 " ideal model delta sigma weight residual 123.12 129.06 -5.94 1.28e+00 6.08e-01 2.14e+01 angle pdb=" N LEU C 390 " pdb=" CA LEU C 390 " pdb=" C LEU C 390 " ideal model delta sigma weight residual 114.04 108.39 5.65 1.24e+00 6.50e-01 2.08e+01 angle pdb=" C2 NAG E 604 " pdb=" N2 NAG E 604 " pdb=" C7 NAG E 604 " ideal model delta sigma weight residual 123.12 128.91 -5.79 1.28e+00 6.08e-01 2.04e+01 angle pdb=" C2 NAG A 605 " pdb=" N2 NAG A 605 " pdb=" C7 NAG A 605 " ideal model delta sigma weight residual 123.12 128.87 -5.75 1.28e+00 6.08e-01 2.01e+01 ... (remaining 24972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 9799 17.84 - 35.67: 886 35.67 - 53.51: 159 53.51 - 71.34: 31 71.34 - 89.18: 17 Dihedral angle restraints: 10892 sinusoidal: 4584 harmonic: 6308 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual -86.00 -7.65 -78.35 1 1.00e+01 1.00e-02 7.66e+01 dihedral pdb=" CB CYS C 331 " pdb=" SG CYS C 331 " pdb=" SG CYS C 385 " pdb=" CB CYS C 385 " ideal model delta sinusoidal sigma weight residual -86.00 -10.01 -75.99 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" CB CYS C 331 " pdb=" SG CYS C 331 " pdb=" SG CYS C 418 " pdb=" CB CYS C 418 " ideal model delta sinusoidal sigma weight residual -86.00 -152.11 66.11 1 1.00e+01 1.00e-02 5.71e+01 ... (remaining 10889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.314: 2953 0.314 - 0.627: 2 0.627 - 0.941: 1 0.941 - 1.254: 0 1.254 - 1.568: 2 Chirality restraints: 2958 Sorted by residual: chirality pdb=" C1 MAN N 5 " pdb=" O6 MAN N 4 " pdb=" C2 MAN N 5 " pdb=" O5 MAN N 5 " both_signs ideal model delta sigma weight residual False 2.40 0.83 1.57 2.00e-02 2.50e+03 6.15e+03 chirality pdb=" C1 MAN S 6 " pdb=" O6 BMA S 3 " pdb=" C2 MAN S 6 " pdb=" O5 MAN S 6 " both_signs ideal model delta sigma weight residual False 2.40 1.03 1.37 2.00e-02 2.50e+03 4.72e+03 chirality pdb=" C1 MAN S 4 " pdb=" O3 BMA S 3 " pdb=" C2 MAN S 4 " pdb=" O5 MAN S 4 " both_signs ideal model delta sigma weight residual False 2.40 1.64 0.76 2.00e-02 2.50e+03 1.45e+03 ... (remaining 2955 not shown) Planarity restraints: 3139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " -0.325 2.00e-02 2.50e+03 2.76e-01 9.49e+02 pdb=" C7 NAG N 2 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " 0.479 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 608 " -0.285 2.00e-02 2.50e+03 2.40e-01 7.20e+02 pdb=" C7 NAG C 608 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG C 608 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG C 608 " 0.409 2.00e-02 2.50e+03 pdb=" O7 NAG C 608 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 1 " 0.194 2.00e-02 2.50e+03 1.61e-01 3.22e+02 pdb=" C7 NAG S 1 " -0.055 2.00e-02 2.50e+03 pdb=" C8 NAG S 1 " 0.142 2.00e-02 2.50e+03 pdb=" N2 NAG S 1 " -0.260 2.00e-02 2.50e+03 pdb=" O7 NAG S 1 " -0.021 2.00e-02 2.50e+03 ... (remaining 3136 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 322 2.54 - 3.13: 15551 3.13 - 3.72: 26183 3.72 - 4.31: 36118 4.31 - 4.90: 59219 Nonbonded interactions: 137393 Sorted by model distance: nonbonded pdb=" O THR E 278 " pdb=" O6 NAG T 1 " model vdw 1.951 2.440 nonbonded pdb=" OG SER A 256 " pdb=" O LEU A 259 " model vdw 2.085 2.440 nonbonded pdb=" OG SER I 7 " pdb=" OG SER I 22 " model vdw 2.088 2.440 nonbonded pdb=" O THR C 278 " pdb=" O6 NAG Q 1 " model vdw 2.090 2.440 nonbonded pdb=" OG SER I 14 " pdb=" O LYS I 109 " model vdw 2.099 2.440 ... (remaining 137388 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' and (resid 33 through 397 or resid 412 through 503 or resid 601 throu \ gh 609)) selection = (chain 'C' and (resid 33 through 300 or resid 325 through 397 or resid 412 throu \ gh 503 or resid 601 through 609)) selection = (chain 'E' and (resid 33 through 126 or (resid 195 and (name N or name CA or nam \ e C or name O or name CB )) or resid 196 through 300 or resid 325 through 464 or \ (resid 465 and (name N or name CA or name C or name O or name CB or name OG1)) \ or resid 466 through 503 or resid 601 through 609)) } ncs_group { reference = (chain 'B' and (resid 519 through 541 or resid 563 through 654 or (resid 655 and \ (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 519 through 541 or (resid 563 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 655)) selection = (chain 'F' and (resid 519 through 620 or (resid 621 and (name N or name CA or na \ me C or name O or name CB )) or resid 622 through 654 or (resid 655 and (name N \ or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'G' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 104 or (resid 105 and (name N or name CA or name C or name \ O or name CB )) or resid 106 through 111)) selection = (chain 'I' and (resid 1 through 104 or (resid 105 and (name N or name CA or name \ C or name O or name CB )) or resid 106 through 111)) selection = (chain 'K' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 111)) } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' } ncs_group { reference = (chain 'P' and (resid 1 or resid 4 through 6)) selection = (chain 'S' and (resid 2 or resid 5 through 7)) } 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: 6 Type Number sf(0) Gaussians S 108 5.16 5 Cl 3 4.86 5 C 11302 2.51 5 N 3048 2.21 5 O 3542 1.98 5 F 3 1.80 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=0.50 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: 0.010 Normalize map: mean=0, sd=1: 0.980 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: 5.070 Check model and map are aligned: 0.240 Process input model: 44.350 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.160 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 : 0.011 0.116 18386 Z= 0.696 Angle : 0.941 13.436 24977 Z= 0.513 Chirality : 0.070 1.568 2958 Planarity : 0.009 0.276 3102 Dihedral : 13.807 89.178 6713 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.87 % Favored : 87.08 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -5.44 (0.14), residues: 2144 helix: -3.61 (0.18), residues: 369 sheet: -3.10 (0.17), residues: 661 loop : -4.01 (0.14), residues: 1114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 275 time to evaluate : 2.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 286 average time/residue: 0.3620 time to fit residues: 147.0666 Evaluate side-chains 215 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 212 time to evaluate : 2.197 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2923 time to fit residues: 5.3781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 8.9990 chunk 162 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 195 optimal weight: 30.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN A 352 HIS B 640 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 103 GLN E 279 ASN E 352 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN L 65 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 18386 Z= 0.269 Angle : 0.680 11.830 24977 Z= 0.352 Chirality : 0.048 0.327 2958 Planarity : 0.005 0.046 3102 Dihedral : 6.281 60.661 2753 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -4.29 (0.16), residues: 2144 helix: -2.15 (0.23), residues: 378 sheet: -2.57 (0.18), residues: 667 loop : -3.31 (0.15), residues: 1099 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 257 time to evaluate : 1.886 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: 33 outliers final: 14 residues processed: 277 average time/residue: 0.3363 time to fit residues: 136.1618 Evaluate side-chains 239 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 225 time to evaluate : 1.959 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 14 average time/residue: 0.1916 time to fit residues: 7.2132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 132 optimal weight: 0.1980 chunk 53 optimal weight: 20.0000 chunk 195 optimal weight: 1.9990 chunk 211 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 193 optimal weight: 30.0000 chunk 66 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 HIS ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 GLN L 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 18386 Z= 0.262 Angle : 0.637 11.134 24977 Z= 0.329 Chirality : 0.046 0.306 2958 Planarity : 0.004 0.045 3102 Dihedral : 5.964 57.773 2753 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.16), residues: 2144 helix: -1.58 (0.25), residues: 385 sheet: -2.23 (0.19), residues: 669 loop : -3.08 (0.16), residues: 1090 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 247 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 24 residues processed: 294 average time/residue: 0.3306 time to fit residues: 144.0654 Evaluate side-chains 248 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 224 time to evaluate : 1.890 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 3 residues processed: 24 average time/residue: 0.1552 time to fit residues: 9.7190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 193 optimal weight: 30.0000 chunk 147 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** L 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 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 0.074 18386 Z= 0.312 Angle : 0.648 11.513 24977 Z= 0.333 Chirality : 0.046 0.305 2958 Planarity : 0.004 0.056 3102 Dihedral : 5.871 56.224 2753 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer Outliers : 2.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.17), residues: 2144 helix: -1.23 (0.26), residues: 376 sheet: -2.07 (0.19), residues: 673 loop : -2.87 (0.16), residues: 1095 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 240 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 27 residues processed: 278 average time/residue: 0.3252 time to fit residues: 134.9962 Evaluate side-chains 249 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 222 time to evaluate : 2.268 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 2 residues processed: 27 average time/residue: 0.1894 time to fit residues: 12.0799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 173 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 177 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 279 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN L 117 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 18386 Z= 0.303 Angle : 0.652 11.827 24977 Z= 0.331 Chirality : 0.046 0.302 2958 Planarity : 0.004 0.058 3102 Dihedral : 5.765 53.918 2753 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.17), residues: 2144 helix: -1.05 (0.26), residues: 376 sheet: -1.88 (0.20), residues: 665 loop : -2.75 (0.16), residues: 1103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 240 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 15 residues processed: 272 average time/residue: 0.3312 time to fit residues: 133.1019 Evaluate side-chains 232 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 217 time to evaluate : 2.121 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 3 residues processed: 15 average time/residue: 0.1539 time to fit residues: 6.9073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 69 optimal weight: 6.9990 chunk 187 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 208 optimal weight: 0.9980 chunk 172 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN L 39 GLN L 65 GLN L 112 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 18386 Z= 0.206 Angle : 0.627 11.885 24977 Z= 0.319 Chirality : 0.045 0.283 2958 Planarity : 0.004 0.060 3102 Dihedral : 5.515 51.050 2753 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.17), residues: 2144 helix: -0.79 (0.27), residues: 380 sheet: -1.69 (0.20), residues: 645 loop : -2.57 (0.17), residues: 1119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 244 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 20 residues processed: 270 average time/residue: 0.3267 time to fit residues: 131.8261 Evaluate side-chains 243 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 223 time to evaluate : 2.156 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 2 residues processed: 20 average time/residue: 0.1678 time to fit residues: 9.2164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 200 optimal weight: 30.0000 chunk 23 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 117 optimal weight: 0.6980 chunk 175 optimal weight: 20.0000 chunk 116 optimal weight: 0.8980 chunk 207 optimal weight: 0.0770 chunk 129 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 overall best weight: 1.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN E 422 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 18386 Z= 0.205 Angle : 0.631 11.616 24977 Z= 0.317 Chirality : 0.045 0.274 2958 Planarity : 0.004 0.051 3102 Dihedral : 5.350 49.662 2753 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.17), residues: 2144 helix: -0.70 (0.27), residues: 382 sheet: -1.56 (0.21), residues: 660 loop : -2.41 (0.17), residues: 1102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 241 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 260 average time/residue: 0.3303 time to fit residues: 126.5261 Evaluate side-chains 231 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 219 time to evaluate : 1.990 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 12 average time/residue: 0.1873 time to fit residues: 7.1534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 128 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 123 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 141 optimal weight: 0.0970 chunk 102 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 chunk 188 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 18386 Z= 0.196 Angle : 0.649 13.956 24977 Z= 0.325 Chirality : 0.044 0.262 2958 Planarity : 0.004 0.067 3102 Dihedral : 5.218 47.242 2753 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.17), residues: 2144 helix: -0.40 (0.27), residues: 374 sheet: -1.46 (0.21), residues: 645 loop : -2.23 (0.17), residues: 1125 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 237 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 248 average time/residue: 0.3400 time to fit residues: 124.7448 Evaluate side-chains 225 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 217 time to evaluate : 2.056 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 8 average time/residue: 0.1659 time to fit residues: 5.1717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 198 optimal weight: 30.0000 chunk 181 optimal weight: 2.9990 chunk 193 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 59 optimal weight: 0.0070 chunk 174 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 192 optimal weight: 0.0770 chunk 126 optimal weight: 0.8980 overall best weight: 0.5956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 18386 Z= 0.188 Angle : 0.629 12.065 24977 Z= 0.315 Chirality : 0.044 0.257 2958 Planarity : 0.004 0.054 3102 Dihedral : 5.092 45.153 2753 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.18), residues: 2144 helix: -0.32 (0.27), residues: 375 sheet: -1.37 (0.21), residues: 637 loop : -2.08 (0.17), residues: 1132 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 230 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 236 average time/residue: 0.3288 time to fit residues: 115.9154 Evaluate side-chains 227 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 222 time to evaluate : 2.070 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.1582 time to fit residues: 4.2398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 204 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 141 optimal weight: 8.9990 chunk 214 optimal weight: 0.6980 chunk 197 optimal weight: 0.2980 chunk 170 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 104 optimal weight: 0.0870 chunk 135 optimal weight: 9.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 18386 Z= 0.203 Angle : 0.641 11.766 24977 Z= 0.321 Chirality : 0.044 0.307 2958 Planarity : 0.004 0.063 3102 Dihedral : 5.030 43.445 2753 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.18), residues: 2144 helix: -0.26 (0.27), residues: 375 sheet: -1.32 (0.21), residues: 640 loop : -2.03 (0.17), residues: 1129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 231 time to evaluate : 2.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 234 average time/residue: 0.3458 time to fit residues: 119.3038 Evaluate side-chains 231 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 226 time to evaluate : 1.821 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.1640 time to fit residues: 4.3112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 157 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 175 optimal weight: 20.0000 chunk 21 optimal weight: 0.1980 chunk 31 optimal weight: 10.0000 chunk 149 optimal weight: 30.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.097516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.064344 restraints weight = 54323.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.066637 restraints weight = 26365.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.068079 restraints weight = 17426.126| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 18386 Z= 0.264 Angle : 0.652 12.790 24977 Z= 0.327 Chirality : 0.045 0.267 2958 Planarity : 0.004 0.066 3102 Dihedral : 5.107 42.064 2753 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.18), residues: 2144 helix: -0.20 (0.27), residues: 375 sheet: -1.23 (0.21), residues: 647 loop : -2.07 (0.17), residues: 1122 =============================================================================== Job complete usr+sys time: 3424.50 seconds wall clock time: 63 minutes 27.85 seconds (3807.85 seconds total)