Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 06:26:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb3_40289/05_2023/8sb3_40289_neut_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb3_40289/05_2023/8sb3_40289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb3_40289/05_2023/8sb3_40289.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb3_40289/05_2023/8sb3_40289.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb3_40289/05_2023/8sb3_40289_neut_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb3_40289/05_2023/8sb3_40289_neut_trim.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.064 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: 5 Type Number sf(0) Gaussians S 129 5.16 5 C 12543 2.51 5 N 3309 2.21 5 O 4109 1.98 5 H 18600 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 102": "OD1" <-> "OD2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "B ASP 632": "OD1" <-> "OD2" Residue "B GLU 647": "OE1" <-> "OE2" Residue "C GLU 13": "OE1" <-> "OE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 84": "OD1" <-> "OD2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "F ASP 102": "OD1" <-> "OD2" Residue "F TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 381": "OE1" <-> "OE2" Residue "F PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 632": "OD1" <-> "OD2" Residue "G GLU 647": "OE1" <-> "OE2" Residue "G GLU 654": "OE1" <-> "OE2" Residue "H ASP 89": "OD1" <-> "OD2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 91": "OE1" <-> "OE2" Residue "K PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 102": "OD1" <-> "OD2" Residue "K TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 335": "OE1" <-> "OE2" Residue "K GLU 348": "OE1" <-> "OE2" Residue "K TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 466": "OE1" <-> "OE2" Residue "L ASP 632": "OD1" <-> "OD2" Residue "L GLU 634": "OE1" <-> "OE2" Residue "L GLU 647": "OE1" <-> "OE2" Residue "M TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 38690 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 7145 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "B" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1919 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain: "C" Number of atoms: 1942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1942 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "D" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1577 Classifications: {'peptide': 110} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 7145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 7145 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "G" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1919 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain: "H" Number of atoms: 1942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1942 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "I" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1577 Classifications: {'peptide': 110} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 7145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 7145 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "L" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1919 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain: "M" Number of atoms: 1942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1942 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "N" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1577 Classifications: {'peptide': 110} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "E" 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 chiralities: 5 Chain: "J" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "O" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "P" 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 chiralities: 4 Chain: "Q" 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 chiralities: 5 Chain: "R" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "S" 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 chiralities: 6 Chain: "T" 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 chiralities: 5 Chain: "U" 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 chiralities: 5 Chain: "V" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "W" 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 chiralities: 6 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 chiralities: 3 Time building chain proxies: 15.69, per 1000 atoms: 0.41 Number of scatterers: 38690 At special positions: 0 Unit cell: (159.43, 160.5, 135.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 129 16.00 O 4109 8.00 N 3309 7.00 C 12543 6.00 H 18600 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " 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=2.04 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.04 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=2.02 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 G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.04 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.02 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS L 605 " distance=2.03 Simple disulfide: pdb=" SG CYS L 598 " - pdb=" SG CYS L 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " 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 J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN J 8 " - " MAN J 9 " " MAN J 10 " - " MAN J 11 " " MAN O 4 " - " MAN O 5 " " MAN O 5 " - " MAN O 6 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN R 8 " - " MAN R 9 " " MAN R 10 " - " MAN R 11 " " MAN S 4 " - " MAN S 5 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " " MAN V 8 " - " MAN V 9 " " MAN V 10 " - " MAN V 11 " " MAN W 4 " - " MAN W 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA J 3 " - " MAN J 4 " " MAN J 7 " - " MAN J 8 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 8 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " MAN V 7 " - " MAN V 8 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA J 3 " - " MAN J 7 " " MAN J 7 " - " MAN J 10 " " BMA O 3 " - " MAN O 7 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 10 " " BMA S 3 " - " MAN S 6 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 5 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 10 " " BMA W 3 " - " MAN W 6 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG E 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN F 301 " " NAG R 1 " - " ASN F 332 " " NAG S 1 " - " ASN F 156 " " NAG T 1 " - " ASN F 442 " " NAG U 1 " - " ASN K 301 " " NAG V 1 " - " ASN K 332 " " NAG W 1 " - " ASN K 156 " " NAG X 1 " - " ASN K 442 " Time building additional restraints: 30.91 Conformation dependent library (CDL) restraints added in 3.3 seconds 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 42 sheets defined 21.1% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 58 through 61 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.950A pdb=" N ASP A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 150 removed outlier: 4.117A pdb=" N ASN A 138 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 474 through 482 removed outlier: 3.951A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.675A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 580 removed outlier: 3.601A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 596 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.630A pdb=" N ASN B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.800A pdb=" N TRP B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.991A pdb=" N GLN B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 660 " --> pdb=" O ASN B 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 61 through 65 Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'F' and resid 58 through 61 Processing helix chain 'F' and resid 68 through 72 Processing helix chain 'F' and resid 99 through 116 removed outlier: 3.971A pdb=" N ASP F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU F 116 " --> pdb=" O TRP F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 139 removed outlier: 4.104A pdb=" N ASN F 138 " --> pdb=" O THR F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 335 through 353 removed outlier: 3.960A pdb=" N HIS F 352 " --> pdb=" O GLU F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 474 through 482 removed outlier: 3.944A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 543 removed outlier: 3.523A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN G 543 " --> pdb=" O VAL G 539 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 580 removed outlier: 3.511A pdb=" N GLN G 575 " --> pdb=" O TRP G 571 " (cutoff:3.500A) Processing helix chain 'G' and resid 582 through 596 Processing helix chain 'G' and resid 611 through 615 Processing helix chain 'G' and resid 618 through 626 removed outlier: 3.500A pdb=" N ASN G 625 " --> pdb=" O GLU G 621 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 636 removed outlier: 3.599A pdb=" N TRP G 631 " --> pdb=" O THR G 627 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 662 removed outlier: 3.989A pdb=" N GLN G 658 " --> pdb=" O GLU G 654 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP G 659 " --> pdb=" O LYS G 655 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU G 660 " --> pdb=" O ASN G 656 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 Processing helix chain 'I' and resid 81 through 85 Processing helix chain 'K' and resid 58 through 61 Processing helix chain 'K' and resid 68 through 72 Processing helix chain 'K' and resid 99 through 116 removed outlier: 3.999A pdb=" N ASP K 107 " --> pdb=" O GLN K 103 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU K 116 " --> pdb=" O TRP K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 150 removed outlier: 4.109A pdb=" N ASN K 138 " --> pdb=" O THR K 135 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY K 139 " --> pdb=" O VAL K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 335 through 351 Processing helix chain 'K' and resid 368 through 373 Processing helix chain 'K' and resid 387 through 391 Processing helix chain 'K' and resid 474 through 482 removed outlier: 3.983A pdb=" N GLU K 482 " --> pdb=" O ASN K 478 " (cutoff:3.500A) Processing helix chain 'L' and resid 529 through 534 Processing helix chain 'L' and resid 536 through 543 removed outlier: 3.643A pdb=" N GLN L 540 " --> pdb=" O THR L 536 " (cutoff:3.500A) Processing helix chain 'L' and resid 571 through 580 removed outlier: 3.599A pdb=" N GLN L 575 " --> pdb=" O TRP L 571 " (cutoff:3.500A) Processing helix chain 'L' and resid 582 through 596 Processing helix chain 'L' and resid 611 through 615 Processing helix chain 'L' and resid 618 through 626 removed outlier: 3.592A pdb=" N ASN L 625 " --> pdb=" O GLU L 621 " (cutoff:3.500A) Processing helix chain 'L' and resid 627 through 636 removed outlier: 3.937A pdb=" N TRP L 631 " --> pdb=" O THR L 627 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 662 removed outlier: 3.971A pdb=" N GLN L 658 " --> pdb=" O GLU L 654 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'M' and resid 61 through 65 Processing helix chain 'N' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.623A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.750A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.742A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 176 removed outlier: 4.096A pdb=" N SER A 158 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 130 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.805A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 4.149A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 11.542A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.943A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.069A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.834A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.112A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.112A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.834A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.069A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.943A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.542A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LYS A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AB1, first strand: chain 'C' and resid 5 through 6 removed outlier: 3.696A pdb=" N LEU C 83 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.617A pdb=" N ALA C 92 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR C 33 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB4, first strand: chain 'D' and resid 47 through 49 Processing sheet with id=AB5, first strand: chain 'D' and resid 47 through 49 removed outlier: 3.586A pdb=" N TYR D 88 " --> pdb=" O THR D 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.036A pdb=" N VAL F 36 " --> pdb=" O THR G 606 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.727A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AB9, first strand: chain 'F' and resid 91 through 92 removed outlier: 3.722A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 170 through 176 removed outlier: 3.541A pdb=" N LYS F 155 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER F 158 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE F 130 " --> pdb=" O SER F 158 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.828A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 259 through 261 removed outlier: 4.093A pdb=" N GLY F 451 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL F 292 " --> pdb=" O ILE F 449 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 11.596A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 11.948A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 12.095A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 10.823A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.096A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLU F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER F 334 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS F 421 " --> pdb=" O PHE F 382 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 271 through 273 removed outlier: 11.096A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 10.823A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 12.095A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 11.948A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 11.596A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL F 292 " --> pdb=" O ILE F 449 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LYS F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 304 through 308 Processing sheet with id=AC6, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.782A pdb=" N LEU H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.641A pdb=" N ALA H 92 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR H 33 " --> pdb=" O ALA H 99 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AC9, first strand: chain 'I' and resid 47 through 49 Processing sheet with id=AD1, first strand: chain 'I' and resid 47 through 49 removed outlier: 3.598A pdb=" N TYR I 88 " --> pdb=" O THR I 105 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 494 through 499 removed outlier: 5.165A pdb=" N VAL K 36 " --> pdb=" O THR L 606 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 75 through 76 Processing sheet with id=AD4, first strand: chain 'K' and resid 84 through 85 removed outlier: 3.723A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 91 through 92 removed outlier: 3.712A pdb=" N GLU K 91 " --> pdb=" O CYS K 239 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 170 through 176 removed outlier: 3.614A pdb=" N LYS K 155 " --> pdb=" O PHE K 176 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER K 158 " --> pdb=" O ILE K 130 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE K 130 " --> pdb=" O SER K 158 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 202 through 203 removed outlier: 6.808A pdb=" N THR K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 259 through 261 removed outlier: 4.151A pdb=" N GLY K 451 " --> pdb=" O LEU K 260 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL K 292 " --> pdb=" O ILE K 449 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 11.392A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 11.974A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 12.144A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) removed outlier: 10.857A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 11.093A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLU K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER K 334 " --> pdb=" O GLU K 293 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA K 329 " --> pdb=" O CYS K 418 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS K 421 " --> pdb=" O PHE K 382 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE K 382 " --> pdb=" O LYS K 421 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 271 through 273 removed outlier: 11.093A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 10.857A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 12.144A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) removed outlier: 11.974A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 11.392A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL K 292 " --> pdb=" O ILE K 449 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS K 360 " --> pdb=" O PHE K 468 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 304 through 308 Processing sheet with id=AE2, first strand: chain 'M' and resid 5 through 6 removed outlier: 3.671A pdb=" N LEU M 83 " --> pdb=" O VAL M 18 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.619A pdb=" N ALA M 92 " --> pdb=" O VAL M 123 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR M 33 " --> pdb=" O ALA M 99 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 18 through 23 removed outlier: 3.766A pdb=" N SER N 65 " --> pdb=" O THR N 76 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 47 through 49 Processing sheet with id=AE6, first strand: chain 'N' and resid 47 through 49 removed outlier: 3.629A pdb=" N TYR N 88 " --> pdb=" O THR N 105 " (cutoff:3.500A) 685 hydrogen bonds defined for protein. 1737 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: 15.09 Time building geometry restraints manager: 32.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 18597 1.04 - 1.24: 2739 1.24 - 1.44: 6287 1.44 - 1.65: 11319 1.65 - 1.85: 171 Bond restraints: 39113 Sorted by residual: bond pdb=" C1 MAN J 11 " pdb=" O5 MAN J 11 " ideal model delta sigma weight residual 1.399 1.490 -0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C1 MAN R 11 " pdb=" O5 MAN R 11 " ideal model delta sigma weight residual 1.399 1.489 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C2 MAN V 8 " pdb=" O2 MAN V 8 " ideal model delta sigma weight residual 1.407 1.490 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C2 MAN R 8 " pdb=" O2 MAN R 8 " ideal model delta sigma weight residual 1.407 1.485 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C1 MAN R 11 " pdb=" C2 MAN R 11 " ideal model delta sigma weight residual 1.526 1.601 -0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 39108 not shown) Histogram of bond angle deviations from ideal: 97.90 - 105.15: 414 105.15 - 112.41: 44099 112.41 - 119.66: 10728 119.66 - 126.92: 14473 126.92 - 134.17: 333 Bond angle restraints: 70047 Sorted by residual: angle pdb=" N CYS K 131 " pdb=" CA CYS K 131 " pdb=" C CYS K 131 " ideal model delta sigma weight residual 108.49 116.53 -8.04 1.15e+00 7.56e-01 4.89e+01 angle pdb=" N CYS F 131 " pdb=" CA CYS F 131 " pdb=" C CYS F 131 " ideal model delta sigma weight residual 108.49 116.46 -7.97 1.15e+00 7.56e-01 4.80e+01 angle pdb=" C ASN A 67 " pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 121.70 132.51 -10.81 1.80e+00 3.09e-01 3.61e+01 angle pdb=" C ASN F 67 " pdb=" N VAL F 68 " pdb=" CA VAL F 68 " ideal model delta sigma weight residual 121.70 132.43 -10.73 1.80e+00 3.09e-01 3.55e+01 angle pdb=" C ASN K 67 " pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 121.70 132.37 -10.67 1.80e+00 3.09e-01 3.52e+01 ... (remaining 70042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 13975 17.95 - 35.89: 1127 35.89 - 53.84: 224 53.84 - 71.78: 87 71.78 - 89.73: 43 Dihedral angle restraints: 15456 sinusoidal: 7125 harmonic: 8331 Sorted by residual: dihedral pdb=" CA CYS A 131 " pdb=" C CYS A 131 " pdb=" N SER A 132 " pdb=" CA SER A 132 " ideal model delta harmonic sigma weight residual -180.00 -131.52 -48.48 0 5.00e+00 4.00e-02 9.40e+01 dihedral pdb=" CA CYS K 131 " pdb=" C CYS K 131 " pdb=" N SER K 132 " pdb=" CA SER K 132 " ideal model delta harmonic sigma weight residual 180.00 -131.55 -48.45 0 5.00e+00 4.00e-02 9.39e+01 dihedral pdb=" CA CYS F 131 " pdb=" C CYS F 131 " pdb=" N SER F 132 " pdb=" CA SER F 132 " ideal model delta harmonic sigma weight residual 180.00 -131.80 -48.20 0 5.00e+00 4.00e-02 9.29e+01 ... (remaining 15453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2729 0.062 - 0.123: 523 0.123 - 0.185: 100 0.185 - 0.246: 13 0.246 - 0.308: 12 Chirality restraints: 3377 Sorted by residual: chirality pdb=" C1 MAN J 11 " pdb=" O2 MAN J 10 " pdb=" C2 MAN J 11 " pdb=" O5 MAN J 11 " both_signs ideal model delta sigma weight residual False 2.40 2.45 -0.05 2.00e-02 2.50e+03 5.97e+00 chirality pdb=" C1 MAN R 11 " pdb=" O2 MAN R 10 " pdb=" C2 MAN R 11 " pdb=" O5 MAN R 11 " both_signs ideal model delta sigma weight residual False 2.40 2.43 -0.03 2.00e-02 2.50e+03 2.57e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 3374 not shown) Planarity restraints: 5793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 628 " -0.015 2.00e-02 2.50e+03 2.29e-02 2.10e+01 pdb=" CG TRP L 628 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP L 628 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP L 628 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP L 628 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP L 628 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP L 628 " 0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 628 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 628 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP L 628 " -0.014 2.00e-02 2.50e+03 pdb=" HD1 TRP L 628 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 TRP L 628 " 0.000 2.00e-02 2.50e+03 pdb=" HE3 TRP L 628 " -0.004 2.00e-02 2.50e+03 pdb=" HZ2 TRP L 628 " -0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP L 628 " 0.013 2.00e-02 2.50e+03 pdb=" HH2 TRP L 628 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 123 " -0.069 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO A 124 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 123 " 0.069 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO F 124 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO F 124 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO F 124 " 0.057 5.00e-02 4.00e+02 ... (remaining 5790 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 4848 2.26 - 2.84: 83567 2.84 - 3.43: 93051 3.43 - 4.01: 129156 4.01 - 4.60: 195973 Nonbonded interactions: 506595 Sorted by model distance: nonbonded pdb=" O GLU N 52 " pdb=" H SER N 54 " model vdw 1.672 1.850 nonbonded pdb=" O GLU I 52 " pdb=" H SER I 54 " model vdw 1.681 1.850 nonbonded pdb=" O GLU D 52 " pdb=" H SER D 54 " model vdw 1.685 1.850 nonbonded pdb=" OD1 ASN F 300 " pdb=" H LYS F 327 " model vdw 1.689 1.850 nonbonded pdb=" OD1 ASN F 463 " pdb=" H THR F 465 " model vdw 1.693 1.850 ... (remaining 506590 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 'F' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'Q' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'R' selection = chain 'V' } ncs_group { reference = (chain 'O' and (resid 2 or resid 5 through 7)) selection = (chain 'S' and (resid 1 or resid 4 through 6)) selection = (chain 'W' and (resid 1 or resid 4 through 6)) } 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: 1.550 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: 0.560 Extract box with map and model: 10.230 Check model and map are aligned: 0.550 Set scattering table: 0.330 Process input model: 111.390 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.290 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 : 0.007 0.091 20513 Z= 0.441 Angle : 1.041 13.926 27903 Z= 0.525 Chirality : 0.055 0.308 3377 Planarity : 0.006 0.103 3435 Dihedral : 14.160 89.725 7056 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.59 % Favored : 91.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -2.11 (0.16), residues: 2436 helix: -1.35 (0.23), residues: 408 sheet: -1.26 (0.19), residues: 651 loop : -1.46 (0.17), residues: 1377 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 3.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.8440 time to fit residues: 429.2168 Evaluate side-chains 178 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 3.104 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 chunk 220 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 461 ASN G 656 ASN ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 461 ASN L 543 ASN ** M 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 20513 Z= 0.336 Angle : 0.746 11.430 27903 Z= 0.387 Chirality : 0.044 0.211 3377 Planarity : 0.005 0.091 3435 Dihedral : 7.027 44.075 2652 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.22 % Favored : 92.28 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -2.14 (0.16), residues: 2436 helix: -0.95 (0.25), residues: 405 sheet: -1.34 (0.19), residues: 684 loop : -1.58 (0.17), residues: 1347 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 210 time to evaluate : 3.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 213 average time/residue: 0.7699 time to fit residues: 246.0090 Evaluate side-chains 156 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 3.107 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 221 optimal weight: 9.9990 chunk 238 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 219 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 177 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN B 656 ASN ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 119 GLN I 41 HIS L 591 GLN L 656 ASN ** M 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.125 20513 Z= 0.432 Angle : 0.777 10.166 27903 Z= 0.400 Chirality : 0.044 0.248 3377 Planarity : 0.006 0.087 3435 Dihedral : 6.979 43.824 2652 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.52 % Favored : 89.98 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.16), residues: 2436 helix: -1.20 (0.25), residues: 405 sheet: -1.72 (0.19), residues: 621 loop : -1.76 (0.16), residues: 1410 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 3.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.7025 time to fit residues: 194.4900 Evaluate side-chains 133 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 3.258 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 221 optimal weight: 0.9990 chunk 234 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 652 GLN G 656 ASN ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN ** M 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 20513 Z= 0.294 Angle : 0.684 10.675 27903 Z= 0.353 Chirality : 0.042 0.242 3377 Planarity : 0.005 0.090 3435 Dihedral : 6.657 41.814 2652 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.49 % Allowed : 8.13 % Favored : 91.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -2.40 (0.16), residues: 2436 helix: -1.11 (0.25), residues: 405 sheet: -1.67 (0.20), residues: 621 loop : -1.71 (0.16), residues: 1410 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 3.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.7208 time to fit residues: 200.5599 Evaluate side-chains 136 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 3.264 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 162 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 652 GLN G 656 ASN ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 20513 Z= 0.236 Angle : 0.646 10.711 27903 Z= 0.333 Chirality : 0.042 0.233 3377 Planarity : 0.004 0.089 3435 Dihedral : 6.383 40.118 2652 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.49 % Allowed : 8.54 % Favored : 90.97 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.27 (0.16), residues: 2436 helix: -0.95 (0.26), residues: 408 sheet: -1.46 (0.19), residues: 642 loop : -1.70 (0.16), residues: 1386 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 3.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 184 average time/residue: 0.7235 time to fit residues: 204.1038 Evaluate side-chains 140 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 2.919 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5213 time to fit residues: 4.4461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 8.9990 chunk 211 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 123 optimal weight: 0.5980 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 652 GLN L 656 ASN ** M 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.083 20513 Z= 0.416 Angle : 0.754 11.277 27903 Z= 0.384 Chirality : 0.043 0.245 3377 Planarity : 0.005 0.086 3435 Dihedral : 6.584 38.372 2652 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.02 % Favored : 89.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.55 (0.16), residues: 2436 helix: -1.09 (0.25), residues: 408 sheet: -1.74 (0.20), residues: 609 loop : -1.87 (0.15), residues: 1419 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 3.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.6694 time to fit residues: 174.9431 Evaluate side-chains 132 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.102 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 7.9990 chunk 26 optimal weight: 0.1980 chunk 133 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 197 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 234 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 20513 Z= 0.211 Angle : 0.641 11.552 27903 Z= 0.328 Chirality : 0.042 0.221 3377 Planarity : 0.004 0.088 3435 Dihedral : 6.258 37.009 2652 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.49 % Allowed : 8.37 % Favored : 91.13 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.34 (0.16), residues: 2436 helix: -0.85 (0.26), residues: 408 sheet: -1.63 (0.20), residues: 573 loop : -1.75 (0.15), residues: 1455 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 3.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.7076 time to fit residues: 204.3901 Evaluate side-chains 140 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 3.113 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 148 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 184 optimal weight: 0.6980 chunk 213 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 20513 Z= 0.318 Angle : 0.675 12.383 27903 Z= 0.344 Chirality : 0.042 0.225 3377 Planarity : 0.005 0.084 3435 Dihedral : 6.221 35.185 2652 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.52 % Favored : 90.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.40 (0.16), residues: 2436 helix: -0.80 (0.26), residues: 405 sheet: -1.80 (0.20), residues: 627 loop : -1.73 (0.16), residues: 1404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 3.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.6921 time to fit residues: 182.3808 Evaluate side-chains 134 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 3.158 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 218 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 206 optimal weight: 0.7980 chunk 217 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 20513 Z= 0.184 Angle : 0.613 12.390 27903 Z= 0.314 Chirality : 0.042 0.203 3377 Planarity : 0.004 0.086 3435 Dihedral : 5.952 34.101 2652 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.51 % Favored : 92.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.20 (0.16), residues: 2436 helix: -0.63 (0.26), residues: 405 sheet: -1.72 (0.20), residues: 612 loop : -1.58 (0.16), residues: 1419 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.7120 time to fit residues: 200.8746 Evaluate side-chains 139 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 3.138 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 242 optimal weight: 9.9990 chunk 222 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 20513 Z= 0.325 Angle : 0.671 13.149 27903 Z= 0.342 Chirality : 0.042 0.218 3377 Planarity : 0.005 0.081 3435 Dihedral : 6.021 32.905 2652 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.69 % Favored : 89.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.16), residues: 2436 helix: -0.61 (0.26), residues: 405 sheet: -1.78 (0.20), residues: 627 loop : -1.70 (0.16), residues: 1404 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 3.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.7004 time to fit residues: 186.5423 Evaluate side-chains 131 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 3.150 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 193 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 198 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 169 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 113 ASN ** 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 = 0.3615 r_free = 0.3615 target = 0.076116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.059032 restraints weight = 243154.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.061619 restraints weight = 113074.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.063321 restraints weight = 71511.533| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 20513 Z= 0.270 Angle : 0.642 12.988 27903 Z= 0.328 Chirality : 0.042 0.207 3377 Planarity : 0.004 0.082 3435 Dihedral : 5.985 32.661 2652 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.24 % Favored : 90.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.16), residues: 2436 helix: -0.56 (0.26), residues: 405 sheet: -1.78 (0.20), residues: 612 loop : -1.68 (0.16), residues: 1419 =============================================================================== Job complete usr+sys time: 6256.62 seconds wall clock time: 113 minutes 42.17 seconds (6822.17 seconds total)