Starting phenix.real_space_refine on Thu Nov 16 22:08:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flw_29288/11_2023/8flw_29288_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flw_29288/11_2023/8flw_29288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flw_29288/11_2023/8flw_29288.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flw_29288/11_2023/8flw_29288.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flw_29288/11_2023/8flw_29288_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flw_29288/11_2023/8flw_29288_updated.pdb" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 119 5.16 5 C 10497 2.51 5 N 2809 2.21 5 O 3443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C ASP 107": "OD1" <-> "OD2" Residue "C GLU 211": "OE1" <-> "OE2" Residue "F GLU 648": "OE1" <-> "OE2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "G GLU 102": "OE1" <-> "OE2" Residue "G TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 482": "OE1" <-> "OE2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 153": "OE1" <-> "OE2" Residue "I GLU 164": "OE1" <-> "OE2" Residue "I ASP 368": "OD1" <-> "OD2" Residue "I ASP 477": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 16868 Number of models: 1 Model: "" Number of chains: 37 Chain: "H" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1102 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "A" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "B" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "C" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "G" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: "O" 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 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "R" 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 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" 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 Chain: "d" 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 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "I" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 9.55, per 1000 atoms: 0.57 Number of scatterers: 16868 At special positions: 0 Unit cell: (132.126, 128.877, 175.446, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 119 16.00 O 3443 8.00 N 2809 7.00 C 10497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.07 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.08 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.04 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " 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 E 4 " - " MAN E 5 " " MAN N 4 " - " MAN N 5 " " MAN Q 4 " - " MAN Q 5 " " MAN X 4 " - " MAN X 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA N 3 " - " MAN N 4 " " BMA Q 3 " - " MAN Q 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA E 3 " - " MAN E 6 " " BMA N 3 " - " MAN N 6 " " BMA Q 3 " - " MAN Q 6 " " BMA X 3 " - " MAN X 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 637 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 156 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 301 " " NAG C 606 " - " ASN C 332 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 355 " " NAG C 609 " - " ASN C 392 " " NAG C 610 " - " ASN C 448 " " NAG D 1 " - " ASN C 197 " " NAG E 1 " - " ASN C 262 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 156 " " NAG G 604 " - " ASN G 234 " " NAG G 605 " - " ASN G 301 " " NAG G 606 " - " ASN G 332 " " NAG G 607 " - " ASN G 339 " " NAG G 608 " - " ASN G 355 " " NAG G 609 " - " ASN G 392 " " NAG G 610 " - " ASN G 448 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 133 " " NAG I 603 " - " ASN I 234 " " NAG I 604 " - " ASN I 301 " " NAG I 605 " - " ASN I 332 " " NAG I 606 " - " ASN I 339 " " NAG I 607 " - " ASN I 355 " " NAG I 608 " - " ASN I 392 " " NAG I 609 " - " ASN I 137 " " NAG J 1 " - " ASN C 295 " " NAG K 1 " - " ASN C 363 " " NAG M 1 " - " ASN C 386 " " NAG N 1 " - " ASN C 160 " " NAG O 1 " - " ASN C 276 " " NAG P 1 " - " ASN G 197 " " NAG Q 1 " - " ASN G 262 " " NAG R 1 " - " ASN G 276 " " NAG S 1 " - " ASN G 295 " " NAG T 1 " - " ASN G 363 " " NAG U 1 " - " ASN G 386 " " NAG V 1 " - " ASN G 160 " " NAG W 1 " - " ASN I 197 " " NAG X 1 " - " ASN I 262 " " NAG Y 1 " - " ASN I 276 " " NAG Z 1 " - " ASN I 295 " " NAG a 1 " - " ASN I 363 " " NAG b 1 " - " ASN I 386 " " NAG c 1 " - " ASN I 448 " " NAG d 1 " - " ASN I 160 " " NAG e 1 " - " ASN I 156 " Time building additional restraints: 8.25 Conformation dependent library (CDL) restraints added in 2.9 seconds 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3672 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 35 sheets defined 21.4% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 59 through 61 No H-bonds generated for 'chain 'H' and resid 59 through 61' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'A' and resid 530 through 543 removed outlier: 3.940A pdb=" N MET A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL A 539 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 594 removed outlier: 3.674A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A 575 " --> pdb=" O TRP A 571 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 621 No H-bonds generated for 'chain 'A' and resid 619 through 621' Processing helix chain 'A' and resid 628 through 634 removed outlier: 3.690A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 663 removed outlier: 3.669A pdb=" N THR A 639 " --> pdb=" O SER A 636 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLN A 640 " --> pdb=" O ASN A 637 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 643 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN A 650 " --> pdb=" O GLU A 647 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN A 652 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN A 656 " --> pdb=" O GLN A 653 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 657 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 543 removed outlier: 3.900A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 595 removed outlier: 3.645A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 590 " --> pdb=" O TYR B 586 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 595 " --> pdb=" O GLN B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 621 No H-bonds generated for 'chain 'B' and resid 619 through 621' Processing helix chain 'B' and resid 628 through 634 removed outlier: 3.645A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 638 No H-bonds generated for 'chain 'B' and resid 636 through 638' Processing helix chain 'B' and resid 640 through 662 removed outlier: 3.717A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.700A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 194 through 197 removed outlier: 3.827A pdb=" N ASN C 197 " --> pdb=" O ILE C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 335 through 350 removed outlier: 3.705A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.806A pdb=" N ASN C 478 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER C 481 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 543 removed outlier: 3.790A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU F 537 " --> pdb=" O ALA F 533 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL F 539 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 596 removed outlier: 3.607A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 623 No H-bonds generated for 'chain 'F' and resid 620 through 623' Processing helix chain 'F' and resid 628 through 634 removed outlier: 3.644A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 660 removed outlier: 3.895A pdb=" N THR F 639 " --> pdb=" O SER F 636 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLN F 640 " --> pdb=" O ASN F 637 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE F 641 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN F 650 " --> pdb=" O GLU F 647 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS F 655 " --> pdb=" O GLN F 652 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 63 Processing helix chain 'G' and resid 99 through 115 Processing helix chain 'G' and resid 335 through 353 removed outlier: 4.008A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE G 353 " --> pdb=" O LEU G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 389 No H-bonds generated for 'chain 'G' and resid 387 through 389' Processing helix chain 'G' and resid 477 through 483 removed outlier: 3.522A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 63 No H-bonds generated for 'chain 'I' and resid 61 through 63' Processing helix chain 'I' and resid 71 through 73 No H-bonds generated for 'chain 'I' and resid 71 through 73' Processing helix chain 'I' and resid 99 through 116 removed outlier: 3.618A pdb=" N THR I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU I 116 " --> pdb=" O TRP I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 125 No H-bonds generated for 'chain 'I' and resid 123 through 125' Processing helix chain 'I' and resid 178 through 180 No H-bonds generated for 'chain 'I' and resid 178 through 180' Processing helix chain 'I' and resid 194 through 197 removed outlier: 4.135A pdb=" N ASN I 197 " --> pdb=" O ILE I 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 194 through 197' Processing helix chain 'I' and resid 335 through 349 removed outlier: 3.799A pdb=" N GLU I 340 " --> pdb=" O ALA I 336 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR I 341 " --> pdb=" O THR I 337 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 372 No H-bonds generated for 'chain 'I' and resid 369 through 372' Processing helix chain 'I' and resid 387 through 389 No H-bonds generated for 'chain 'I' and resid 387 through 389' Processing helix chain 'I' and resid 475 through 483 removed outlier: 3.931A pdb=" N ASN I 478 " --> pdb=" O MET I 475 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER I 481 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'H' and resid 4 through 6 removed outlier: 4.052A pdb=" N VAL H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS H 23 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL H 18 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU H 82 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL H 20 " --> pdb=" O MET H 80 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU H 81 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR H 68 " --> pdb=" O GLU H 81 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 55 through 57 removed outlier: 4.328A pdb=" N GLY H 56 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP H 50 " --> pdb=" O GLY H 56 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS H 35 " --> pdb=" O LEU H 93 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU H 93 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR H 104 " --> pdb=" O SER H 96 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 88 through 90 removed outlier: 3.633A pdb=" N ALA H 88 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 100 through 100E removed outlier: 6.687A pdb=" N GLU H 100O" --> pdb=" O ASP H 100B" (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE H 100D" --> pdb=" O TYR H 100M" (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR H 100M" --> pdb=" O PHE H 100D" (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.939A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 19 through 21 removed outlier: 3.513A pdb=" N ALA L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE L 75 " --> pdb=" O ALA L 19 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER L 65 " --> pdb=" O THR L 72 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 102 through 104 removed outlier: 3.569A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL L 104 " --> pdb=" O GLY L 84 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR L 36 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU L 46 " --> pdb=" O LEU L 37 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= I, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.992A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= K, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.886A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 130 through 133 Processing sheet with id= M, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= N, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.654A pdb=" N MET C 271 " --> pdb=" O GLN C 287 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 443 through 449 removed outlier: 3.972A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL C 292 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE C 376 " --> pdb=" O PHE C 383 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 304 through 308 Processing sheet with id= Q, first strand: chain 'G' and resid 35 through 40 Processing sheet with id= R, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.205A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 91 through 94 removed outlier: 4.225A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE G 93 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 130 through 133 Processing sheet with id= U, first strand: chain 'G' and resid 181 through 183 Processing sheet with id= V, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.643A pdb=" N MET G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU G 452 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N ALA G 362 " --> pdb=" O PRO G 470 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE G 359 " --> pdb=" O TRP G 395 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 414 through 417 removed outlier: 3.531A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE G 294 " --> pdb=" O SER G 447 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 304 through 309 removed outlier: 3.791A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 374 through 377 Processing sheet with id= Z, first strand: chain 'I' and resid 45 through 47 removed outlier: 4.594A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 53 through 55 Processing sheet with id= AB, first strand: chain 'I' and resid 91 through 94 removed outlier: 4.012A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE I 93 " --> pdb=" O GLY I 237 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'I' and resid 130 through 133 Processing sheet with id= AD, first strand: chain 'I' and resid 181 through 183 Processing sheet with id= AE, first strand: chain 'I' and resid 271 through 273 Processing sheet with id= AF, first strand: chain 'I' and resid 443 through 449 removed outlier: 4.199A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL I 292 " --> pdb=" O ILE I 449 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 305 through 309 removed outlier: 3.696A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 358 through 362 removed outlier: 4.303A pdb=" N THR I 467 " --> pdb=" O ASP I 457 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'I' and resid 374 through 378 removed outlier: 3.696A pdb=" N GLU I 381 " --> pdb=" O CYS I 378 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.38 Time building geometry restraints manager: 8.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2655 1.29 - 1.43: 4464 1.43 - 1.56: 9910 1.56 - 1.70: 2 1.70 - 1.83: 157 Bond restraints: 17188 Sorted by residual: bond pdb=" C MET I 161 " pdb=" O MET I 161 " ideal model delta sigma weight residual 1.234 1.160 0.074 1.28e-02 6.10e+03 3.30e+01 bond pdb=" C PRO C 124 " pdb=" O PRO C 124 " ideal model delta sigma weight residual 1.236 1.172 0.064 1.20e-02 6.94e+03 2.88e+01 bond pdb=" CA ALA C 319 " pdb=" CB ALA C 319 " ideal model delta sigma weight residual 1.535 1.457 0.079 1.71e-02 3.42e+03 2.12e+01 bond pdb=" OH TYS H 100F" pdb=" S TYS H 100F" ideal model delta sigma weight residual 1.679 1.590 0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" N PRO C 124 " pdb=" CA PRO C 124 " ideal model delta sigma weight residual 1.468 1.423 0.045 1.10e-02 8.26e+03 1.67e+01 ... (remaining 17183 not shown) Histogram of bond angle deviations from ideal: 97.39 - 104.73: 239 104.73 - 112.06: 9253 112.06 - 119.40: 5677 119.40 - 126.74: 7839 126.74 - 134.08: 325 Bond angle restraints: 23333 Sorted by residual: angle pdb=" C THR C 320 " pdb=" CA THR C 320 " pdb=" CB THR C 320 " ideal model delta sigma weight residual 110.19 98.32 11.87 1.64e+00 3.72e-01 5.24e+01 angle pdb=" CA MET I 161 " pdb=" C MET I 161 " pdb=" O MET I 161 " ideal model delta sigma weight residual 121.58 113.61 7.97 1.16e+00 7.43e-01 4.72e+01 angle pdb=" C ASN C 262 " pdb=" CA ASN C 262 " pdb=" CB ASN C 262 " ideal model delta sigma weight residual 111.89 120.76 -8.87 1.42e+00 4.96e-01 3.90e+01 angle pdb=" CA ASN C 262 " pdb=" CB ASN C 262 " pdb=" CG ASN C 262 " ideal model delta sigma weight residual 112.60 118.55 -5.95 1.00e+00 1.00e+00 3.54e+01 angle pdb=" C TYS H 100F" pdb=" CA TYS H 100F" pdb=" CB TYS H 100F" ideal model delta sigma weight residual 110.10 99.40 10.70 1.90e+00 2.77e-01 3.17e+01 ... (remaining 23328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 8583 18.00 - 35.99: 749 35.99 - 53.99: 168 53.99 - 71.98: 33 71.98 - 89.98: 17 Dihedral angle restraints: 9550 sinusoidal: 3872 harmonic: 5678 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 165.49 -72.49 1 1.00e+01 1.00e-02 6.71e+01 dihedral pdb=" CB CYS I 119 " pdb=" SG CYS I 119 " pdb=" SG CYS I 205 " pdb=" CB CYS I 205 " ideal model delta sinusoidal sigma weight residual -86.00 -147.39 61.39 1 1.00e+01 1.00e-02 5.00e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -146.06 60.06 1 1.00e+01 1.00e-02 4.81e+01 ... (remaining 9547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 2884 0.156 - 0.312: 36 0.312 - 0.467: 2 0.467 - 0.623: 0 0.623 - 0.779: 1 Chirality restraints: 2923 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.23e+02 chirality pdb=" C1 MAN E 5 " pdb=" O2 MAN E 4 " pdb=" C2 MAN E 5 " pdb=" O5 MAN E 5 " both_signs ideal model delta sigma weight residual False 2.40 2.60 -0.20 2.00e-02 2.50e+03 1.02e+02 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.68e+01 ... (remaining 2920 not shown) Planarity restraints: 2892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.257 2.00e-02 2.50e+03 2.20e-01 6.03e+02 pdb=" C7 NAG E 1 " -0.050 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.029 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.368 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.190 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 2 " -0.103 2.00e-02 2.50e+03 8.54e-02 9.12e+01 pdb=" C7 NAG O 2 " 0.025 2.00e-02 2.50e+03 pdb=" C8 NAG O 2 " -0.076 2.00e-02 2.50e+03 pdb=" N2 NAG O 2 " 0.139 2.00e-02 2.50e+03 pdb=" O7 NAG O 2 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP C 427 " 0.023 2.00e-02 2.50e+03 4.75e-02 2.26e+01 pdb=" C TRP C 427 " -0.082 2.00e-02 2.50e+03 pdb=" O TRP C 427 " 0.031 2.00e-02 2.50e+03 pdb=" N GLN C 428 " 0.028 2.00e-02 2.50e+03 ... (remaining 2889 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 17 2.29 - 2.95: 8076 2.95 - 3.60: 21851 3.60 - 4.25: 35834 4.25 - 4.90: 60608 Nonbonded interactions: 126386 Sorted by model distance: nonbonded pdb=" OG SER C 447 " pdb=" C1 NAG E 1 " model vdw 1.644 3.470 nonbonded pdb=" O ASP B 632 " pdb=" OG SER B 636 " model vdw 2.084 2.440 nonbonded pdb=" O THR C 123 " pdb=" OG1 THR C 123 " model vdw 2.113 2.440 nonbonded pdb=" OG1 THR A 627 " pdb=" OE1 GLN A 630 " model vdw 2.174 2.440 nonbonded pdb=" O SER C 460 " pdb=" OG1 THR C 461 " model vdw 2.181 2.440 ... (remaining 126381 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 33 through 505 or resid 601 through 609)) selection = (chain 'G' and (resid 33 through 505 or resid 601 through 609)) selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'e' } ncs_group { reference = chain 'E' selection = chain 'N' selection = chain 'Q' selection = chain 'X' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'V' selection = chain 'c' selection = chain 'd' } 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.160 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 48.410 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.250 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: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 17188 Z= 0.315 Angle : 0.801 11.874 23333 Z= 0.419 Chirality : 0.056 0.779 2923 Planarity : 0.006 0.220 2834 Dihedral : 14.310 89.978 5767 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.45 % Favored : 95.29 % Rotamer: Outliers : 0.81 % Allowed : 0.64 % Favored : 98.56 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1931 helix: 1.40 (0.31), residues: 336 sheet: -0.01 (0.23), residues: 557 loop : -0.38 (0.20), residues: 1038 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 371 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 381 average time/residue: 0.3059 time to fit residues: 172.2157 Evaluate side-chains 214 residues out of total 1735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 208 time to evaluate : 1.890 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2123 time to fit residues: 4.7513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN L 93 HIS A 543 ASN B 543 ASN B 625 ASN C 105 HIS C 185 ASN C 203 GLN F 630 GLN G 99 ASN ** G 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 ASN I 114 GLN I 374 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17188 Z= 0.324 Angle : 0.693 9.957 23333 Z= 0.333 Chirality : 0.049 0.406 2923 Planarity : 0.004 0.052 2834 Dihedral : 4.206 35.128 2100 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.83 % Allowed : 9.82 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.19), residues: 1931 helix: 0.57 (0.28), residues: 336 sheet: 0.26 (0.24), residues: 517 loop : -0.49 (0.19), residues: 1078 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 225 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 37 residues processed: 256 average time/residue: 0.2838 time to fit residues: 110.4582 Evaluate side-chains 221 residues out of total 1735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 184 time to evaluate : 2.016 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1564 time to fit residues: 13.4945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 148 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 chunk 192 optimal weight: 0.6980 chunk 158 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 143 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 HIS ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17188 Z= 0.184 Angle : 0.590 10.703 23333 Z= 0.282 Chirality : 0.045 0.378 2923 Planarity : 0.003 0.045 2834 Dihedral : 4.044 29.549 2100 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.50 % Allowed : 13.57 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.19), residues: 1931 helix: 0.24 (0.28), residues: 348 sheet: 0.03 (0.23), residues: 556 loop : -0.42 (0.20), residues: 1027 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 1.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 8 residues processed: 226 average time/residue: 0.3022 time to fit residues: 103.5044 Evaluate side-chains 199 residues out of total 1735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 191 time to evaluate : 1.984 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1602 time to fit residues: 5.0309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 2.9990 chunk 134 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 0.0030 chunk 189 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 HIS C 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17188 Z= 0.220 Angle : 0.597 9.986 23333 Z= 0.283 Chirality : 0.046 0.421 2923 Planarity : 0.003 0.037 2834 Dihedral : 4.095 23.995 2100 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.73 % Allowed : 15.65 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.19), residues: 1931 helix: 0.20 (0.28), residues: 348 sheet: -0.14 (0.22), residues: 574 loop : -0.41 (0.20), residues: 1009 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 205 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 220 average time/residue: 0.2787 time to fit residues: 94.2185 Evaluate side-chains 208 residues out of total 1735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 192 time to evaluate : 1.879 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1510 time to fit residues: 7.1450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 2 optimal weight: 0.0030 chunk 141 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 590 GLN C 99 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17188 Z= 0.202 Angle : 0.587 10.057 23333 Z= 0.279 Chirality : 0.045 0.417 2923 Planarity : 0.003 0.026 2834 Dihedral : 4.089 25.131 2100 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.27 % Allowed : 16.86 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.19), residues: 1931 helix: 0.25 (0.29), residues: 342 sheet: 0.10 (0.23), residues: 517 loop : -0.56 (0.19), residues: 1072 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 203 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 221 average time/residue: 0.2891 time to fit residues: 97.7305 Evaluate side-chains 208 residues out of total 1735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 197 time to evaluate : 2.062 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1626 time to fit residues: 6.0708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 2.9990 chunk 170 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN G 85 HIS ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 478 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17188 Z= 0.298 Angle : 0.651 11.032 23333 Z= 0.308 Chirality : 0.047 0.412 2923 Planarity : 0.003 0.047 2834 Dihedral : 4.377 25.395 2100 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.62 % Allowed : 18.65 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.19), residues: 1931 helix: -0.09 (0.28), residues: 357 sheet: 0.00 (0.23), residues: 517 loop : -0.68 (0.19), residues: 1057 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 201 time to evaluate : 1.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 18 residues processed: 218 average time/residue: 0.2965 time to fit residues: 97.6734 Evaluate side-chains 204 residues out of total 1735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 186 time to evaluate : 1.937 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1561 time to fit residues: 7.7915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.9980 chunk 21 optimal weight: 0.0970 chunk 108 optimal weight: 0.0060 chunk 138 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 105 optimal weight: 0.0070 chunk 188 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 87 optimal weight: 0.4980 overall best weight: 0.3212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17188 Z= 0.142 Angle : 0.585 10.939 23333 Z= 0.275 Chirality : 0.045 0.418 2923 Planarity : 0.003 0.036 2834 Dihedral : 4.163 27.848 2100 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.40 % Allowed : 19.92 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.19), residues: 1931 helix: 0.20 (0.28), residues: 357 sheet: 0.02 (0.22), residues: 544 loop : -0.50 (0.19), residues: 1030 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 214 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 219 average time/residue: 0.3016 time to fit residues: 99.6430 Evaluate side-chains 199 residues out of total 1735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 2.011 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1933 time to fit residues: 2.9673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.6980 chunk 75 optimal weight: 0.3980 chunk 112 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17188 Z= 0.276 Angle : 0.633 10.126 23333 Z= 0.299 Chirality : 0.047 0.401 2923 Planarity : 0.003 0.061 2834 Dihedral : 4.287 27.234 2100 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.98 % Allowed : 20.61 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.19), residues: 1931 helix: 0.12 (0.28), residues: 357 sheet: 0.12 (0.23), residues: 517 loop : -0.67 (0.19), residues: 1057 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 198 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 207 average time/residue: 0.2954 time to fit residues: 92.6871 Evaluate side-chains 200 residues out of total 1735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 192 time to evaluate : 1.922 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1982 time to fit residues: 5.2810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 175 optimal weight: 0.0270 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17188 Z= 0.193 Angle : 0.606 13.193 23333 Z= 0.285 Chirality : 0.045 0.386 2923 Planarity : 0.003 0.065 2834 Dihedral : 4.238 28.537 2100 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.40 % Allowed : 20.73 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.19), residues: 1931 helix: -0.07 (0.28), residues: 375 sheet: -0.03 (0.22), residues: 544 loop : -0.49 (0.19), residues: 1012 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 199 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 201 average time/residue: 0.2947 time to fit residues: 90.0384 Evaluate side-chains 193 residues out of total 1735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 190 time to evaluate : 1.762 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1454 time to fit residues: 3.2564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.0570 chunk 186 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 195 optimal weight: 0.5980 chunk 179 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 GLN ** I 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17188 Z= 0.183 Angle : 0.598 9.935 23333 Z= 0.281 Chirality : 0.045 0.382 2923 Planarity : 0.003 0.061 2834 Dihedral : 4.164 29.417 2100 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.35 % Allowed : 21.02 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.19), residues: 1931 helix: 0.00 (0.28), residues: 375 sheet: -0.01 (0.22), residues: 544 loop : -0.50 (0.19), residues: 1012 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 202 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 203 average time/residue: 0.2930 time to fit residues: 90.2135 Evaluate side-chains 198 residues out of total 1735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 193 time to evaluate : 1.877 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1790 time to fit residues: 4.0042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 0.0570 chunk 165 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 143 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 159 optimal weight: 0.0770 chunk 19 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 6 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.166474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.133034 restraints weight = 23874.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.137099 restraints weight = 18969.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.138921 restraints weight = 14171.775| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17188 Z= 0.167 Angle : 0.585 9.911 23333 Z= 0.275 Chirality : 0.045 0.388 2923 Planarity : 0.003 0.028 2834 Dihedral : 4.140 29.968 2100 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.12 % Allowed : 21.65 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.19), residues: 1931 helix: -0.02 (0.28), residues: 387 sheet: -0.00 (0.22), residues: 544 loop : -0.47 (0.19), residues: 1000 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3164.98 seconds wall clock time: 59 minutes 9.20 seconds (3549.20 seconds total)