Starting phenix.real_space_refine on Sun Mar 17 03:55:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtt_21383/03_2024/6vtt_21383_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtt_21383/03_2024/6vtt_21383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtt_21383/03_2024/6vtt_21383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtt_21383/03_2024/6vtt_21383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtt_21383/03_2024/6vtt_21383_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtt_21383/03_2024/6vtt_21383_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 10385 2.51 5 N 2712 2.21 5 O 3400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 46": "NH1" <-> "NH2" Residue "F PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "F ARG 171": "NH1" <-> "NH2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 308": "NH1" <-> "NH2" Residue "F TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 344": "NH1" <-> "NH2" Residue "F PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 370": "OE1" <-> "OE2" Residue "F PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 432": "NH1" <-> "NH2" Residue "F PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 469": "NH1" <-> "NH2" Residue "F TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 503": "NH1" <-> "NH2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 133": "OD1" <-> "OD2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E ARG 171": "NH1" <-> "NH2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 308": "NH1" <-> "NH2" Residue "E TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 344": "NH1" <-> "NH2" Residue "E TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 432": "NH1" <-> "NH2" Residue "E ARG 469": "NH1" <-> "NH2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 503": "NH1" <-> "NH2" Residue "G ARG 46": "NH1" <-> "NH2" Residue "G PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 151": "NH1" <-> "NH2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "G ARG 171": "NH1" <-> "NH2" Residue "G TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 308": "NH1" <-> "NH2" Residue "G ASP 321": "OD1" <-> "OD2" Residue "G ARG 344": "NH1" <-> "NH2" Residue "G PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 432": "NH1" <-> "NH2" Residue "G ARG 469": "NH1" <-> "NH2" Residue "G ARG 503": "NH1" <-> "NH2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 52": "OD1" <-> "OD2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 633": "NH1" <-> "NH2" Residue "A GLU 647": "OE1" <-> "OE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 633": "NH1" <-> "NH2" Residue "B ASP 640": "OD1" <-> "OD2" Residue "C PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 633": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16607 Number of models: 1 Model: "" Number of chains: 36 Chain: "F" Number of atoms: 3400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3400 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 5 Chain: "E" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3410 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 22, 'TRANS': 408} Chain breaks: 5 Chain: "G" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3448 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 5 Chain: "H" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1138 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} 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: "L" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 797 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "A" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "B" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1026 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "C" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1012 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "D" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" 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: 9 Unresolved non-hydrogen chiralities: 3 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" 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: 15 Unresolved non-hydrogen chiralities: 5 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" 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: 12 Unresolved non-hydrogen chiralities: 4 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" 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: 18 Unresolved non-hydrogen chiralities: 6 Chain: "W" 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: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" 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: 9 Unresolved non-hydrogen chiralities: 3 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" 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: 18 Unresolved non-hydrogen chiralities: 6 Chain: "c" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "E" 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 dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.99, per 1000 atoms: 0.54 Number of scatterers: 16607 At special positions: 0 Unit cell: (128.244, 128.244, 167.703, 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 110 16.00 O 3400 8.00 N 2712 7.00 C 10385 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.04 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " 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=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 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 C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.04 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 100A" - pdb=" SG CYS H 100Q" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 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 ALPHA1-2 " MAN b 4 " - " MAN b 5 " ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 6 " " MAN V 4 " - " MAN V 5 " " BMA W 3 " - " MAN W 4 " " BMA b 3 " - " MAN b 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 5 " " BMA b 3 " - " MAN b 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1611 " - " ASN A 611 " " NAG A1637 " - " ASN A 637 " " NAG B1611 " - " ASN B 611 " " NAG B1637 " - " ASN B 637 " " NAG C1611 " - " ASN C 611 " " NAG C1637 " - " ASN C 637 " " NAG D 1 " - " ASN F 130 " " NAG E1088 " - " ASN E 88 " " NAG E1130 " - " ASN E 130 " " NAG E1156 " - " ASN E 156 " " NAG E1160 " - " ASN E 160 " " NAG E1230 " - " ASN E 230 " " NAG E1241 " - " ASN E 241 " " NAG E1276 " - " ASN E 276 " " NAG E1289 " - " ASN E 289 " " NAG E1301 " - " ASN E 301 " " NAG E1332 " - " ASN E 332 " " NAG E1356 " - " ASN E 356 " " NAG E1362 " - " ASN E 362 " " NAG E1442 " - " ASN E 442 " " NAG E1443 " - " ASN E 448 " " NAG E1502 " - " ASN E 502 " " NAG F1088 " - " ASN F 88 " " NAG F1234 " - " ASN F 234 " " NAG F1289 " - " ASN F 289 " " NAG F1301 " - " ASN F 301 " " NAG F1356 " - " ASN F 356 " " NAG F1362 " - " ASN F 362 " " NAG F1386 " - " ASN F 386 " " NAG F1442 " - " ASN F 442 " " NAG F1448 " - " ASN F 448 " " NAG F1502 " - " ASN F 502 " " NAG G1088 " - " ASN G 88 " " NAG G1234 " - " ASN G 234 " " NAG G1276 " - " ASN G 276 " " NAG G1301 " - " ASN G 301 " " NAG G1356 " - " ASN G 356 " " NAG G1362 " - " ASN G 362 " " NAG G1386 " - " ASN G 386 " " NAG G1442 " - " ASN G 442 " " NAG G1448 " - " ASN G 448 " " NAG G1502 " - " ASN G 502 " " NAG I 1 " - " ASN F 156 " " NAG J 1 " - " ASN F 160 " " NAG K 1 " - " ASN F 197 " " NAG M 1 " - " ASN F 230 " " NAG N 1 " - " ASN F 241 " " NAG O 1 " - " ASN F 262 " " NAG P 1 " - " ASN F 276 " " NAG Q 1 " - " ASN F 332 " " NAG R 1 " - " ASN E 197 " " NAG S 1 " - " ASN E 234 " " NAG T 1 " - " ASN E 262 " " NAG U 1 " - " ASN E 386 " " NAG V 1 " - " ASN G 130 " " NAG W 1 " - " ASN G 156 " " NAG X 1 " - " ASN G 160 " " NAG Y 1 " - " ASN G 197 " " NAG Z 1 " - " ASN G 230 " " NAG a 1 " - " ASN G 241 " " NAG b 1 " - " ASN G 262 " " NAG c 1 " - " ASN G 289 " " NAG d 1 " - " ASN G 332 " Time building additional restraints: 7.41 Conformation dependent library (CDL) restraints added in 2.6 seconds 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3582 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 37 sheets defined 18.4% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'F' and resid 100 through 116 removed outlier: 3.569A pdb=" N HIS F 105 " --> pdb=" O VAL F 101 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE F 109 " --> pdb=" O HIS F 105 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER F 110 " --> pdb=" O GLU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 352 removed outlier: 3.649A pdb=" N THR F 341 " --> pdb=" O LYS F 337 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG F 344 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL F 345 " --> pdb=" O THR F 341 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG F 350 " --> pdb=" O SER F 346 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU F 351 " --> pdb=" O GLU F 347 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N HIS F 352 " --> pdb=" O LYS F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 428 No H-bonds generated for 'chain 'F' and resid 426 through 428' Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'E' and resid 100 through 117 removed outlier: 3.959A pdb=" N SER E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 336 through 339 No H-bonds generated for 'chain 'E' and resid 336 through 339' Processing helix chain 'E' and resid 341 through 348 removed outlier: 3.575A pdb=" N SER E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 428 No H-bonds generated for 'chain 'E' and resid 426 through 428' Processing helix chain 'E' and resid 476 through 480 Processing helix chain 'G' and resid 100 through 116 removed outlier: 3.686A pdb=" N GLU G 106 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP G 113 " --> pdb=" O ILE G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 335 through 353 removed outlier: 3.910A pdb=" N ARG G 344 " --> pdb=" O LYS G 340 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU G 347 " --> pdb=" O GLN G 343 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU G 349 " --> pdb=" O VAL G 345 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG G 350 " --> pdb=" O SER G 346 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU G 351 " --> pdb=" O GLU G 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 428 No H-bonds generated for 'chain 'G' and resid 426 through 428' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 61 through 63 No H-bonds generated for 'chain 'H' and resid 61 through 63' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'A' and resid 514 through 525 removed outlier: 3.936A pdb=" N PHE A 519 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 521 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE A 522 " --> pdb=" O VAL A 518 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU A 523 " --> pdb=" O PHE A 519 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ALA A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 541 removed outlier: 4.306A pdb=" N SER A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N THR A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 539 " --> pdb=" O ASN A 535 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 595 removed outlier: 3.710A pdb=" N LEU A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 635 removed outlier: 3.530A pdb=" N ASP A 632 " --> pdb=" O TRP A 628 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG A 633 " --> pdb=" O MET A 629 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 628 through 635' Processing helix chain 'A' and resid 639 through 658 removed outlier: 3.855A pdb=" N LYS A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 645 " --> pdb=" O THR A 641 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 655 " --> pdb=" O PHE A 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 541 removed outlier: 4.338A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASN B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL B 539 " --> pdb=" O ASN B 535 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 594 removed outlier: 3.735A pdb=" N GLU B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 624 No H-bonds generated for 'chain 'B' and resid 622 through 624' Processing helix chain 'B' and resid 628 through 638 removed outlier: 3.548A pdb=" N ASP B 632 " --> pdb=" O TRP B 628 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ASN B 637 " --> pdb=" O ARG B 633 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TYR B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 657 removed outlier: 3.804A pdb=" N LEU B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 519 removed outlier: 3.689A pdb=" N PHE C 519 " --> pdb=" O LEU C 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 514 through 519' Processing helix chain 'C' and resid 533 through 542 removed outlier: 3.935A pdb=" N LEU C 537 " --> pdb=" O ALA C 533 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N THR C 538 " --> pdb=" O SER C 534 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL C 539 " --> pdb=" O ASN C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 594 removed outlier: 3.558A pdb=" N LYS C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN C 575 " --> pdb=" O TRP C 571 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU C 576 " --> pdb=" O GLY C 572 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 589 " --> pdb=" O ARG C 585 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 593 " --> pdb=" O VAL C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 622 No H-bonds generated for 'chain 'C' and resid 619 through 622' Processing helix chain 'C' and resid 628 through 632 Processing helix chain 'C' and resid 640 through 660 removed outlier: 3.620A pdb=" N LEU C 645 " --> pdb=" O THR C 641 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN C 660 " --> pdb=" O ASN C 656 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'F' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.592A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'F' and resid 130 through 133 Processing sheet with id= D, first strand: chain 'F' and resid 160 through 162 Processing sheet with id= E, first strand: chain 'F' and resid 271 through 273 Processing sheet with id= F, first strand: chain 'F' and resid 444 through 449 removed outlier: 3.833A pdb=" N ILE F 294 " --> pdb=" O SER F 447 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL F 292 " --> pdb=" O ILE F 449 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLU F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER F 334 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS F 330 " --> pdb=" O THR F 297 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 358 through 361 Processing sheet with id= H, first strand: chain 'F' and resid 374 through 378 removed outlier: 3.742A pdb=" N CYS F 385 " --> pdb=" O HIS F 374 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 181 through 185 removed outlier: 7.452A pdb=" N GLU F 190 " --> pdb=" O LEU F 184 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 304 through 312 removed outlier: 3.507A pdb=" N PHE F 317 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE F 309 " --> pdb=" O GLN F 315 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= L, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.655A pdb=" N THR E 244 " --> pdb=" O LEU E 84 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 91 through 93 removed outlier: 4.387A pdb=" N PHE E 93 " --> pdb=" O GLY E 237 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 154 through 162 Processing sheet with id= O, first strand: chain 'E' and resid 271 through 273 Processing sheet with id= P, first strand: chain 'E' and resid 292 through 297 removed outlier: 3.975A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS E 296 " --> pdb=" O CYS E 445 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 304 through 308 Processing sheet with id= R, first strand: chain 'E' and resid 359 through 361 removed outlier: 6.160A pdb=" N GLU E 466 " --> pdb=" O ILE E 360 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 376 through 378 Processing sheet with id= T, first strand: chain 'E' and resid 181 through 185 removed outlier: 7.842A pdb=" N GLU E 190 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 35 through 40 Processing sheet with id= V, first strand: chain 'G' and resid 45 through 47 Processing sheet with id= W, first strand: chain 'G' and resid 154 through 162 Processing sheet with id= X, first strand: chain 'G' and resid 181 through 183 Processing sheet with id= Y, first strand: chain 'G' and resid 201 through 203 removed outlier: 5.945A pdb=" N ALA G 433 " --> pdb=" O THR G 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.630A pdb=" N ILE G 271 " --> pdb=" O HIS G 287 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 444 through 449 removed outlier: 3.665A pdb=" N CYS G 445 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS G 296 " --> pdb=" O CYS G 445 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 304 through 308 Processing sheet with id= AC, first strand: chain 'G' and resid 359 through 362 removed outlier: 6.026A pdb=" N GLU G 466 " --> pdb=" O ILE G 360 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASN G 362 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE G 468 " --> pdb=" O ASN G 362 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'G' and resid 382 through 385 removed outlier: 4.174A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.421A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.826A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.726A pdb=" N THR H 68 " --> pdb=" O GLN H 81 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 91 through 94 removed outlier: 3.628A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 100 through 100C removed outlier: 6.735A pdb=" N LYS H 100S" --> pdb=" O GLU H 100B" (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 19 through 24 removed outlier: 4.410A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'L' and resid 85 through 90 removed outlier: 6.338A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) 347 hydrogen bonds defined for protein. 966 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: 4.34 Time building geometry restraints manager: 7.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5123 1.34 - 1.47: 4326 1.47 - 1.60: 7326 1.60 - 1.73: 2 1.73 - 1.86: 144 Bond restraints: 16921 Sorted by residual: bond pdb=" O2 TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.461 1.635 -0.174 2.00e-02 2.50e+03 7.55e+01 bond pdb=" O1 TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.462 1.634 -0.172 2.00e-02 2.50e+03 7.37e+01 bond pdb=" OH TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.679 1.543 0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" OH TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.679 1.548 0.131 2.00e-02 2.50e+03 4.26e+01 bond pdb=" N GLU H 100C" pdb=" CA GLU H 100C" ideal model delta sigma weight residual 1.460 1.486 -0.026 1.17e-02 7.31e+03 5.03e+00 ... (remaining 16916 not shown) Histogram of bond angle deviations from ideal: 85.86 - 95.49: 6 95.49 - 105.12: 270 105.12 - 114.74: 11108 114.74 - 124.37: 11207 124.37 - 133.99: 368 Bond angle restraints: 22959 Sorted by residual: angle pdb=" O2 TYS H 100H" pdb=" S TYS H 100H" pdb=" O3 TYS H 100H" ideal model delta sigma weight residual 115.38 86.69 28.69 3.00e+00 1.11e-01 9.14e+01 angle pdb=" O1 TYS H 100I" pdb=" S TYS H 100I" pdb=" O3 TYS H 100I" ideal model delta sigma weight residual 115.16 86.70 28.46 3.00e+00 1.11e-01 9.00e+01 angle pdb=" O1 TYS H 100I" pdb=" S TYS H 100I" pdb=" O2 TYS H 100I" ideal model delta sigma weight residual 114.11 85.86 28.25 3.00e+00 1.11e-01 8.86e+01 angle pdb=" O1 TYS H 100H" pdb=" S TYS H 100H" pdb=" O2 TYS H 100H" ideal model delta sigma weight residual 114.11 86.76 27.35 3.00e+00 1.11e-01 8.31e+01 angle pdb=" OH TYS H 100I" pdb=" S TYS H 100I" pdb=" O3 TYS H 100I" ideal model delta sigma weight residual 100.21 119.65 -19.44 3.00e+00 1.11e-01 4.20e+01 ... (remaining 22954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.40: 10786 22.40 - 44.80: 495 44.80 - 67.20: 108 67.20 - 89.60: 46 89.60 - 112.00: 28 Dihedral angle restraints: 11463 sinusoidal: 5922 harmonic: 5541 Sorted by residual: dihedral pdb=" C ARG F 192 " pdb=" N ARG F 192 " pdb=" CA ARG F 192 " pdb=" CB ARG F 192 " ideal model delta harmonic sigma weight residual -122.60 -105.76 -16.84 0 2.50e+00 1.60e-01 4.54e+01 dihedral pdb=" CB CYS G 378 " pdb=" SG CYS G 378 " pdb=" SG CYS G 445 " pdb=" CB CYS G 445 " ideal model delta sinusoidal sigma weight residual -86.00 -133.75 47.75 1 1.00e+01 1.00e-02 3.15e+01 dihedral pdb=" CB CYS G 218 " pdb=" SG CYS G 218 " pdb=" SG CYS G 247 " pdb=" CB CYS G 247 " ideal model delta sinusoidal sigma weight residual 93.00 48.59 44.41 1 1.00e+01 1.00e-02 2.74e+01 ... (remaining 11460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2678 0.095 - 0.189: 179 0.189 - 0.284: 17 0.284 - 0.378: 3 0.378 - 0.473: 3 Chirality restraints: 2880 Sorted by residual: chirality pdb=" C1 MAN V 6 " pdb=" O3 BMA V 3 " pdb=" C2 MAN V 6 " pdb=" O5 MAN V 6 " both_signs ideal model delta sigma weight residual False 2.40 1.99 0.41 2.00e-02 2.50e+03 4.24e+02 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.38e+02 chirality pdb=" C1 MAN V 4 " pdb=" O6 BMA V 3 " pdb=" C2 MAN V 4 " pdb=" O5 MAN V 4 " both_signs ideal model delta sigma weight residual False 2.40 2.23 0.17 2.00e-02 2.50e+03 6.88e+01 ... (remaining 2877 not shown) Planarity restraints: 2839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 2 " -0.367 2.00e-02 2.50e+03 3.15e-01 1.24e+03 pdb=" C7 NAG V 2 " 0.091 2.00e-02 2.50e+03 pdb=" C8 NAG V 2 " -0.102 2.00e-02 2.50e+03 pdb=" N2 NAG V 2 " 0.558 2.00e-02 2.50e+03 pdb=" O7 NAG V 2 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G1088 " -0.120 2.00e-02 2.50e+03 9.65e-02 1.16e+02 pdb=" C7 NAG G1088 " 0.034 2.00e-02 2.50e+03 pdb=" C8 NAG G1088 " -0.090 2.00e-02 2.50e+03 pdb=" N2 NAG G1088 " 0.149 2.00e-02 2.50e+03 pdb=" O7 NAG G1088 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 87 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.78e+00 pdb=" C GLU G 87 " 0.038 2.00e-02 2.50e+03 pdb=" O GLU G 87 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN G 88 " -0.013 2.00e-02 2.50e+03 ... (remaining 2836 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1930 2.75 - 3.29: 15606 3.29 - 3.83: 25061 3.83 - 4.36: 28917 4.36 - 4.90: 50126 Nonbonded interactions: 121640 Sorted by model distance: nonbonded pdb=" O4 MAN V 6 " pdb=" O6 MAN V 6 " model vdw 2.214 2.440 nonbonded pdb=" OG1 THR F 37 " pdb=" O CYS A 604 " model vdw 2.220 2.440 nonbonded pdb=" OE1 GLN F 258 " pdb=" OG1 THR F 387 " model vdw 2.230 2.440 nonbonded pdb=" OE1 GLN E 363 " pdb=" OG SER E 388 " model vdw 2.253 2.440 nonbonded pdb=" OE1 GLU E 164 " pdb=" CB ASN G 197 " model vdw 2.271 3.440 ... (remaining 121635 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' and (resid 513 through 566 or resid 568 through 660 or resid 1611 thr \ ough 1637)) selection = (chain 'C' and (resid 513 through 544 or resid 568 through 660 or resid 1611 thr \ ough 1637)) } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 34 through 60 or resid 65 through 135 or resid 152 through \ 186 or resid 189 through 394 or resid 411 through 504 or resid 1130 through 133 \ 2)) selection = (chain 'F' and (resid 34 through 60 or resid 65 through 186 or resid 189 through \ 459 or resid 464 through 504 or resid 1234 through 1502)) selection = (chain 'G' and (resid 34 through 135 or resid 152 through 394 or resid 411 throu \ gh 459 or resid 464 through 504 or resid 1088 through 1448)) } ncs_group { reference = chain 'K' selection = chain 'X' } ncs_group { reference = chain 'O' selection = chain 'W' } ncs_group { reference = chain 'V' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 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: 0.010 Extract box with map and model: 7.150 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 44.100 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 : 0.005 0.174 16921 Z= 0.288 Angle : 0.825 28.688 22959 Z= 0.351 Chirality : 0.052 0.473 2880 Planarity : 0.007 0.315 2776 Dihedral : 14.724 112.005 7782 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Cbeta Deviations : 0.17 % 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: -4.61 (0.15), residues: 1872 helix: -4.20 (0.13), residues: 330 sheet: -2.46 (0.21), residues: 433 loop : -3.05 (0.15), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 338 HIS 0.002 0.000 HIS E 374 PHE 0.008 0.001 PHE F 233 TYR 0.004 0.001 TYR G 484 ARG 0.003 0.000 ARG F 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 195 ASN cc_start: 0.7974 (p0) cc_final: 0.7636 (p0) REVERT: F 217 TYR cc_start: 0.7698 (m-10) cc_final: 0.7463 (m-10) REVERT: E 107 ASP cc_start: 0.7943 (t0) cc_final: 0.7533 (t0) REVERT: E 258 GLN cc_start: 0.8273 (mt0) cc_final: 0.8054 (mt0) REVERT: H 28 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7662 (ptp90) REVERT: H 30 ASP cc_start: 0.8593 (p0) cc_final: 0.8103 (p0) REVERT: H 32 TYR cc_start: 0.6782 (m-80) cc_final: 0.6176 (m-10) REVERT: H 34 MET cc_start: 0.8396 (mmm) cc_final: 0.7953 (mpp) REVERT: H 38 ARG cc_start: 0.6893 (ptt180) cc_final: 0.5756 (ptp-170) REVERT: H 39 GLN cc_start: 0.7360 (tt0) cc_final: 0.6746 (tt0) REVERT: H 48 VAL cc_start: 0.5732 (t) cc_final: 0.5486 (t) REVERT: H 51 ILE cc_start: 0.9073 (tt) cc_final: 0.8407 (mm) REVERT: H 64 TRP cc_start: 0.6877 (m-10) cc_final: 0.6364 (m-90) REVERT: H 101 ILE cc_start: 0.8644 (mm) cc_final: 0.8404 (pt) REVERT: L 50 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7970 (tm-30) REVERT: L 87 TYR cc_start: 0.5341 (m-80) cc_final: 0.4553 (m-80) REVERT: B 584 GLU cc_start: 0.8215 (tp30) cc_final: 0.7999 (mm-30) REVERT: B 595 MET cc_start: 0.7380 (mtm) cc_final: 0.7063 (mtm) REVERT: C 607 ASN cc_start: 0.8543 (t0) cc_final: 0.8247 (t0) REVERT: C 620 ASN cc_start: 0.8115 (t0) cc_final: 0.7747 (t0) REVERT: C 657 GLU cc_start: 0.9039 (tp30) cc_final: 0.8812 (tt0) REVERT: C 658 LYS cc_start: 0.8386 (mmtt) cc_final: 0.8154 (mptt) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.3565 time to fit residues: 99.4643 Evaluate side-chains 128 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 79 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 90 optimal weight: 0.0020 chunk 110 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 216 HIS G 66 HIS G 330 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 38 GLN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16921 Z= 0.194 Angle : 0.589 9.861 22959 Z= 0.279 Chirality : 0.046 0.262 2880 Planarity : 0.003 0.028 2776 Dihedral : 12.585 89.827 4176 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.59 % Allowed : 9.20 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.17), residues: 1872 helix: -2.09 (0.24), residues: 321 sheet: -2.06 (0.21), residues: 488 loop : -2.63 (0.16), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 35 HIS 0.003 0.001 HIS E 374 PHE 0.012 0.001 PHE F 376 TYR 0.024 0.001 TYR L 36 ARG 0.004 0.000 ARG C 633 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 136 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 195 ASN cc_start: 0.8083 (p0) cc_final: 0.7766 (p0) REVERT: E 192 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7099 (ttm170) REVERT: H 30 ASP cc_start: 0.8637 (p0) cc_final: 0.8106 (p0) REVERT: H 34 MET cc_start: 0.8209 (mmm) cc_final: 0.7928 (mmm) REVERT: H 38 ARG cc_start: 0.7047 (ptt180) cc_final: 0.6419 (ptp-170) REVERT: H 51 ILE cc_start: 0.8871 (tt) cc_final: 0.8468 (mm) REVERT: H 64 TRP cc_start: 0.6904 (m-10) cc_final: 0.6406 (m-90) REVERT: H 66 ARG cc_start: 0.2294 (ptt180) cc_final: 0.1392 (ttm110) REVERT: H 108 MET cc_start: 0.8141 (tpp) cc_final: 0.7878 (tpp) REVERT: L 32 PHE cc_start: 0.7723 (m-80) cc_final: 0.7308 (m-80) REVERT: L 42 ARG cc_start: 0.8495 (mmm-85) cc_final: 0.8281 (mtt90) REVERT: L 87 TYR cc_start: 0.5672 (m-80) cc_final: 0.5252 (m-80) REVERT: A 626 MET cc_start: 0.8862 (ttt) cc_final: 0.8321 (mtp) REVERT: C 607 ASN cc_start: 0.8459 (t0) cc_final: 0.8180 (t0) outliers start: 10 outliers final: 3 residues processed: 142 average time/residue: 0.3089 time to fit residues: 65.2874 Evaluate side-chains 116 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain G residue 123 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 0.4980 chunk 53 optimal weight: 8.9990 chunk 142 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 171 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 137 optimal weight: 20.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 246 GLN L 38 GLN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16921 Z= 0.186 Angle : 0.558 10.202 22959 Z= 0.263 Chirality : 0.046 0.257 2880 Planarity : 0.003 0.067 2776 Dihedral : 10.991 82.125 4176 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.12 % Allowed : 12.09 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.18), residues: 1872 helix: -1.16 (0.27), residues: 328 sheet: -1.84 (0.22), residues: 474 loop : -2.38 (0.17), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 35 HIS 0.003 0.001 HIS E 374 PHE 0.013 0.001 PHE B 651 TYR 0.016 0.001 TYR C 638 ARG 0.008 0.000 ARG E 432 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 195 ASN cc_start: 0.8190 (p0) cc_final: 0.7889 (p0) REVERT: E 170 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7628 (ttp80) REVERT: E 192 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7113 (ttm170) REVERT: G 302 MET cc_start: 0.8593 (mmt) cc_final: 0.8257 (mmp) REVERT: H 32 TYR cc_start: 0.6927 (m-80) cc_final: 0.5958 (m-10) REVERT: H 34 MET cc_start: 0.8066 (mmm) cc_final: 0.7808 (mmm) REVERT: H 38 ARG cc_start: 0.7086 (ptt180) cc_final: 0.6525 (ptp90) REVERT: H 51 ILE cc_start: 0.8850 (tt) cc_final: 0.8433 (mm) REVERT: H 64 TRP cc_start: 0.6931 (m-10) cc_final: 0.6426 (m-90) REVERT: H 66 ARG cc_start: 0.2054 (ptt180) cc_final: 0.1561 (ttm170) REVERT: H 98 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7277 (mm-30) REVERT: H 108 MET cc_start: 0.8264 (tpp) cc_final: 0.7998 (tpp) REVERT: L 32 PHE cc_start: 0.7560 (m-80) cc_final: 0.7263 (m-80) REVERT: L 42 ARG cc_start: 0.8609 (mmm-85) cc_final: 0.8390 (mmm-85) REVERT: A 626 MET cc_start: 0.8592 (ttt) cc_final: 0.8358 (mtp) REVERT: C 607 ASN cc_start: 0.8472 (t0) cc_final: 0.8157 (t0) outliers start: 19 outliers final: 11 residues processed: 140 average time/residue: 0.2841 time to fit residues: 61.0016 Evaluate side-chains 124 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 655 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 172 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 67 ASN F 246 GLN F 392 ASN G 229 ASN G 280 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 16921 Z= 0.362 Angle : 0.661 11.130 22959 Z= 0.314 Chirality : 0.048 0.273 2880 Planarity : 0.004 0.039 2776 Dihedral : 10.253 75.389 4176 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 1.89 % Allowed : 14.34 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.18), residues: 1872 helix: -0.77 (0.29), residues: 323 sheet: -1.85 (0.22), residues: 477 loop : -2.31 (0.17), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 571 HIS 0.006 0.001 HIS E 374 PHE 0.018 0.002 PHE G 391 TYR 0.015 0.001 TYR C 638 ARG 0.016 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 114 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9338 (tp) cc_final: 0.9056 (tp) REVERT: E 170 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7515 (ttp80) REVERT: E 192 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7198 (ttm170) REVERT: G 125 LEU cc_start: 0.9308 (tp) cc_final: 0.9071 (tp) REVERT: G 302 MET cc_start: 0.8683 (mmt) cc_final: 0.8319 (mmp) REVERT: H 32 TYR cc_start: 0.6918 (m-80) cc_final: 0.5981 (m-10) REVERT: H 34 MET cc_start: 0.8031 (mmm) cc_final: 0.7797 (mmm) REVERT: H 38 ARG cc_start: 0.6950 (ptt180) cc_final: 0.6268 (ptp90) REVERT: H 51 ILE cc_start: 0.8882 (tt) cc_final: 0.8473 (mm) REVERT: H 64 TRP cc_start: 0.7002 (m-10) cc_final: 0.6441 (m-10) REVERT: H 66 ARG cc_start: 0.2117 (ptt180) cc_final: 0.1770 (ttp-110) REVERT: H 91 TYR cc_start: 0.7296 (m-80) cc_final: 0.7017 (m-80) REVERT: H 98 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7391 (mm-30) REVERT: H 108 MET cc_start: 0.8215 (tpp) cc_final: 0.7948 (tpp) REVERT: L 32 PHE cc_start: 0.7523 (m-80) cc_final: 0.7221 (m-80) REVERT: L 42 ARG cc_start: 0.8641 (mmm-85) cc_final: 0.8383 (mmm-85) REVERT: A 626 MET cc_start: 0.8771 (ttt) cc_final: 0.8163 (mtp) REVERT: C 607 ASN cc_start: 0.8595 (t0) cc_final: 0.8193 (t0) REVERT: C 612 SER cc_start: 0.8739 (m) cc_final: 0.8318 (t) outliers start: 32 outliers final: 21 residues processed: 140 average time/residue: 0.2930 time to fit residues: 62.2460 Evaluate side-chains 132 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain C residue 661 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 136 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 16921 Z= 0.360 Angle : 0.662 10.909 22959 Z= 0.314 Chirality : 0.048 0.283 2880 Planarity : 0.004 0.055 2776 Dihedral : 9.794 66.645 4176 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.07 % Allowed : 15.63 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.18), residues: 1872 helix: -0.65 (0.29), residues: 329 sheet: -1.77 (0.22), residues: 471 loop : -2.23 (0.17), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 571 HIS 0.005 0.001 HIS E 374 PHE 0.018 0.002 PHE G 391 TYR 0.014 0.001 TYR C 638 ARG 0.008 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 119 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 125 LEU cc_start: 0.9358 (tp) cc_final: 0.9053 (tp) REVERT: E 170 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7539 (ttp80) REVERT: E 192 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7193 (ttm170) REVERT: E 258 GLN cc_start: 0.8345 (mt0) cc_final: 0.8057 (mt0) REVERT: H 34 MET cc_start: 0.7965 (mmm) cc_final: 0.7339 (mpp) REVERT: H 38 ARG cc_start: 0.6871 (ptt180) cc_final: 0.6232 (ptp-170) REVERT: H 51 ILE cc_start: 0.8958 (tt) cc_final: 0.8425 (mm) REVERT: H 64 TRP cc_start: 0.6794 (m-10) cc_final: 0.6214 (m-10) REVERT: H 82 MET cc_start: 0.5108 (mmm) cc_final: 0.4808 (mmp) REVERT: H 91 TYR cc_start: 0.7236 (m-80) cc_final: 0.6989 (m-80) REVERT: H 98 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7405 (mm-30) REVERT: H 99 ASP cc_start: 0.7394 (p0) cc_final: 0.7180 (p0) REVERT: L 32 PHE cc_start: 0.7469 (m-80) cc_final: 0.7167 (m-80) REVERT: L 42 ARG cc_start: 0.8645 (mmm-85) cc_final: 0.8363 (mmm-85) REVERT: A 626 MET cc_start: 0.8794 (ttt) cc_final: 0.8218 (mtp) REVERT: C 607 ASN cc_start: 0.8628 (t0) cc_final: 0.8148 (t0) REVERT: C 612 SER cc_start: 0.8795 (m) cc_final: 0.8365 (t) outliers start: 52 outliers final: 39 residues processed: 159 average time/residue: 0.2892 time to fit residues: 69.4574 Evaluate side-chains 153 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 111 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 80 ASN Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 661 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 36 optimal weight: 0.0670 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 182 optimal weight: 2.9990 chunk 151 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 15 optimal weight: 0.0030 chunk 60 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 overall best weight: 0.5530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 229 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16921 Z= 0.141 Angle : 0.552 9.875 22959 Z= 0.259 Chirality : 0.045 0.264 2880 Planarity : 0.003 0.031 2776 Dihedral : 8.860 60.934 4176 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.18 % Allowed : 16.87 % Favored : 80.94 % 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: -2.38 (0.19), residues: 1872 helix: -0.23 (0.30), residues: 328 sheet: -1.67 (0.22), residues: 478 loop : -2.01 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 571 HIS 0.003 0.001 HIS F 216 PHE 0.017 0.001 PHE E 210 TYR 0.016 0.001 TYR C 638 ARG 0.005 0.000 ARG C 633 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 125 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 97 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8447 (ptmt) REVERT: F 234 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8437 (p0) REVERT: E 170 ARG cc_start: 0.7753 (ttp80) cc_final: 0.7527 (ttp80) REVERT: E 290 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7980 (pm20) REVERT: H 34 MET cc_start: 0.7924 (mmm) cc_final: 0.7269 (mpp) REVERT: H 38 ARG cc_start: 0.6802 (ptt180) cc_final: 0.6326 (ptp90) REVERT: H 51 ILE cc_start: 0.8845 (tt) cc_final: 0.8287 (mm) REVERT: H 64 TRP cc_start: 0.6829 (m-10) cc_final: 0.6274 (m-10) REVERT: H 91 TYR cc_start: 0.7151 (m-80) cc_final: 0.6913 (m-80) REVERT: H 98 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7407 (mm-30) REVERT: H 108 MET cc_start: 0.8021 (tpp) cc_final: 0.7643 (tpp) REVERT: L 32 PHE cc_start: 0.7402 (m-80) cc_final: 0.7088 (m-80) REVERT: L 42 ARG cc_start: 0.8749 (mmm-85) cc_final: 0.8441 (mmm-85) REVERT: L 46 LEU cc_start: 0.8741 (pt) cc_final: 0.8126 (tt) REVERT: A 626 MET cc_start: 0.8754 (ttt) cc_final: 0.8155 (mtp) REVERT: B 626 MET cc_start: 0.8250 (tpp) cc_final: 0.8025 (ttt) REVERT: C 612 SER cc_start: 0.8810 (m) cc_final: 0.8336 (t) outliers start: 37 outliers final: 21 residues processed: 153 average time/residue: 0.2820 time to fit residues: 65.6392 Evaluate side-chains 138 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 632 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 195 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16921 Z= 0.314 Angle : 0.631 11.316 22959 Z= 0.297 Chirality : 0.047 0.281 2880 Planarity : 0.003 0.042 2776 Dihedral : 8.706 66.219 4176 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.01 % Allowed : 17.17 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.19), residues: 1872 helix: -0.23 (0.30), residues: 323 sheet: -1.69 (0.22), residues: 475 loop : -2.00 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP C 571 HIS 0.005 0.001 HIS E 374 PHE 0.017 0.002 PHE G 390A TYR 0.011 0.001 TYR C 586 ARG 0.003 0.000 ARG E 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 111 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 234 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8495 (p0) REVERT: E 170 ARG cc_start: 0.7758 (ttp80) cc_final: 0.7445 (ttp80) REVERT: E 258 GLN cc_start: 0.8365 (mt0) cc_final: 0.8053 (mt0) REVERT: E 290 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.6934 (pp20) REVERT: G 302 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8515 (mmp) REVERT: H 34 MET cc_start: 0.7931 (mmm) cc_final: 0.7437 (mpp) REVERT: H 38 ARG cc_start: 0.6805 (ptt180) cc_final: 0.6291 (ptp90) REVERT: H 51 ILE cc_start: 0.8876 (tt) cc_final: 0.8268 (mm) REVERT: H 64 TRP cc_start: 0.6889 (m-10) cc_final: 0.6247 (m-10) REVERT: H 91 TYR cc_start: 0.7247 (m-80) cc_final: 0.6999 (m-80) REVERT: H 98 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7426 (mm-30) REVERT: H 108 MET cc_start: 0.8203 (tpp) cc_final: 0.7861 (tpp) REVERT: L 32 PHE cc_start: 0.7501 (m-80) cc_final: 0.7174 (m-80) REVERT: L 42 ARG cc_start: 0.8775 (mmm-85) cc_final: 0.8525 (mmm-85) REVERT: L 46 LEU cc_start: 0.8751 (pt) cc_final: 0.8128 (tt) REVERT: A 626 MET cc_start: 0.8784 (ttt) cc_final: 0.8192 (mtp) REVERT: C 612 SER cc_start: 0.8960 (m) cc_final: 0.8531 (t) outliers start: 51 outliers final: 40 residues processed: 151 average time/residue: 0.2739 time to fit residues: 64.0905 Evaluate side-chains 150 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 106 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 80 ASN Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 425 ASN Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 362 ASN Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 302 MET Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 661 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 0.7980 chunk 72 optimal weight: 0.1980 chunk 108 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 143 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16921 Z= 0.152 Angle : 0.562 10.167 22959 Z= 0.263 Chirality : 0.045 0.270 2880 Planarity : 0.003 0.033 2776 Dihedral : 8.221 62.973 4176 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.18 % Allowed : 18.05 % Favored : 79.76 % 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: -2.16 (0.19), residues: 1872 helix: -0.00 (0.30), residues: 328 sheet: -1.54 (0.23), residues: 478 loop : -1.88 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP C 571 HIS 0.003 0.001 HIS F 216 PHE 0.015 0.001 PHE G 390A TYR 0.016 0.001 TYR C 638 ARG 0.008 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 114 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 234 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8440 (p0) REVERT: E 290 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.6820 (pp20) REVERT: H 34 MET cc_start: 0.7875 (mmm) cc_final: 0.7373 (mpp) REVERT: H 38 ARG cc_start: 0.6817 (ptt180) cc_final: 0.6304 (ptp90) REVERT: H 51 ILE cc_start: 0.8945 (tt) cc_final: 0.8351 (mm) REVERT: H 64 TRP cc_start: 0.6788 (m-10) cc_final: 0.6177 (m-10) REVERT: H 91 TYR cc_start: 0.7208 (m-80) cc_final: 0.7002 (m-80) REVERT: H 98 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7414 (mm-30) REVERT: H 108 MET cc_start: 0.8164 (tpp) cc_final: 0.7753 (tpp) REVERT: L 32 PHE cc_start: 0.7496 (m-80) cc_final: 0.7150 (m-80) REVERT: L 42 ARG cc_start: 0.8786 (mmm-85) cc_final: 0.8456 (mmm-85) REVERT: L 46 LEU cc_start: 0.8731 (pt) cc_final: 0.8133 (tt) REVERT: A 626 MET cc_start: 0.8735 (ttt) cc_final: 0.8127 (mtp) REVERT: C 612 SER cc_start: 0.8897 (m) cc_final: 0.8422 (t) outliers start: 37 outliers final: 29 residues processed: 141 average time/residue: 0.2721 time to fit residues: 59.2535 Evaluate side-chains 138 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 106 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 425 ASN Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 362 ASN Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 632 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 169 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 133 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16921 Z= 0.159 Angle : 0.559 10.341 22959 Z= 0.261 Chirality : 0.045 0.264 2880 Planarity : 0.003 0.034 2776 Dihedral : 7.940 63.626 4176 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.48 % Allowed : 17.76 % Favored : 79.76 % 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: -2.06 (0.19), residues: 1872 helix: 0.16 (0.31), residues: 322 sheet: -1.51 (0.23), residues: 472 loop : -1.81 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP C 571 HIS 0.003 0.001 HIS F 216 PHE 0.014 0.001 PHE G 390A TYR 0.014 0.001 TYR C 638 ARG 0.007 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 116 time to evaluate : 1.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 234 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8447 (p0) REVERT: E 170 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7693 (ttp-170) REVERT: E 290 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.6804 (pp20) REVERT: H 34 MET cc_start: 0.7866 (mmm) cc_final: 0.7431 (mpp) REVERT: H 38 ARG cc_start: 0.6809 (ptt180) cc_final: 0.6290 (ptp90) REVERT: H 51 ILE cc_start: 0.8972 (tt) cc_final: 0.8441 (mm) REVERT: H 64 TRP cc_start: 0.6867 (m-10) cc_final: 0.6246 (m-10) REVERT: H 98 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7344 (mm-30) REVERT: H 108 MET cc_start: 0.8147 (tpp) cc_final: 0.7757 (tpp) REVERT: L 32 PHE cc_start: 0.7508 (m-80) cc_final: 0.7140 (m-80) REVERT: L 42 ARG cc_start: 0.8774 (mmm-85) cc_final: 0.8453 (mmm-85) REVERT: L 46 LEU cc_start: 0.8712 (pt) cc_final: 0.8113 (tt) REVERT: A 626 MET cc_start: 0.8720 (ttt) cc_final: 0.8112 (mtp) REVERT: A 629 MET cc_start: 0.8525 (tpt) cc_final: 0.8316 (tpt) REVERT: C 612 SER cc_start: 0.8886 (m) cc_final: 0.8420 (t) REVERT: C 659 ASP cc_start: 0.5203 (m-30) cc_final: 0.4494 (p0) outliers start: 42 outliers final: 33 residues processed: 151 average time/residue: 0.2711 time to fit residues: 63.6148 Evaluate side-chains 146 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 109 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 80 ASN Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 425 ASN Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 362 ASN Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain C residue 632 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 173 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 chunk 15 optimal weight: 0.0030 chunk 115 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16921 Z= 0.167 Angle : 0.558 10.650 22959 Z= 0.261 Chirality : 0.045 0.265 2880 Planarity : 0.003 0.033 2776 Dihedral : 7.795 63.626 4176 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.42 % Allowed : 17.99 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.19), residues: 1872 helix: 0.33 (0.31), residues: 322 sheet: -1.40 (0.23), residues: 468 loop : -1.77 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 35 HIS 0.003 0.001 HIS F 216 PHE 0.012 0.001 PHE G 390A TYR 0.013 0.001 TYR C 638 ARG 0.007 0.000 ARG H 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 113 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 428 GLN cc_start: 0.7668 (pm20) cc_final: 0.7456 (pm20) REVERT: E 290 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.6825 (pp20) REVERT: H 34 MET cc_start: 0.7909 (mmm) cc_final: 0.7432 (mpp) REVERT: H 38 ARG cc_start: 0.6820 (ptt180) cc_final: 0.6289 (ptp90) REVERT: H 51 ILE cc_start: 0.8932 (tt) cc_final: 0.8437 (mm) REVERT: H 64 TRP cc_start: 0.6832 (m-10) cc_final: 0.6218 (m-10) REVERT: H 98 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7350 (mm-30) REVERT: H 108 MET cc_start: 0.8220 (tpp) cc_final: 0.7836 (tpp) REVERT: L 32 PHE cc_start: 0.7495 (m-80) cc_final: 0.7147 (m-80) REVERT: L 42 ARG cc_start: 0.8772 (mmm-85) cc_final: 0.8452 (mmm-85) REVERT: L 46 LEU cc_start: 0.8797 (pt) cc_final: 0.8190 (tt) REVERT: A 626 MET cc_start: 0.8720 (ttt) cc_final: 0.8395 (mtp) REVERT: C 612 SER cc_start: 0.8885 (m) cc_final: 0.8419 (t) outliers start: 41 outliers final: 36 residues processed: 149 average time/residue: 0.2650 time to fit residues: 62.0779 Evaluate side-chains 147 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 109 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 80 ASN Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 362 ASN Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 150 optimal weight: 40.0000 chunk 62 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.090406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.069571 restraints weight = 44258.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.071709 restraints weight = 26187.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.073125 restraints weight = 18733.011| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 16921 Z= 0.364 Angle : 0.675 11.721 22959 Z= 0.319 Chirality : 0.049 0.368 2880 Planarity : 0.004 0.048 2776 Dihedral : 8.313 68.166 4176 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.77 % Allowed : 17.88 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.19), residues: 1872 helix: 0.10 (0.30), residues: 323 sheet: -1.61 (0.23), residues: 482 loop : -1.81 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 35 HIS 0.005 0.001 HIS E 374 PHE 0.022 0.002 PHE E 53 TYR 0.017 0.001 TYR C 638 ARG 0.004 0.000 ARG H 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2650.36 seconds wall clock time: 49 minutes 38.30 seconds (2978.30 seconds total)