Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 11:10:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orp_20177/04_2023/6orp_20177.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orp_20177/04_2023/6orp_20177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orp_20177/04_2023/6orp_20177.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orp_20177/04_2023/6orp_20177.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orp_20177/04_2023/6orp_20177.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orp_20177/04_2023/6orp_20177.pdb" } resolution = 4.4 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= 0.204 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 114 5.16 5 C 12487 2.51 5 N 3317 2.21 5 O 4054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 456": "NH1" <-> "NH2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "C TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 327": "NH1" <-> "NH2" Residue "G ARG 456": "NH1" <-> "NH2" Residue "G ARG 469": "NH1" <-> "NH2" Residue "H PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 327": "NH1" <-> "NH2" Residue "I ARG 456": "NH1" <-> "NH2" Residue "I ARG 469": "NH1" <-> "NH2" Residue "J PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 19972 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "B" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3485 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 4 Chain: "C" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "E" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 808 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3485 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 4 Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "I" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3485 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 4 Chain: "J" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 938 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "K" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 808 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 808 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} 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: 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: "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: 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "Z" 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: "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: 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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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: "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: 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: "h" 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: "i" 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: "j" 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: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "l" 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: 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: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 10.58, per 1000 atoms: 0.53 Number of scatterers: 19972 At special positions: 0 Unit cell: (139.292, 133.548, 150.78, 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 114 16.00 O 4054 8.00 N 3317 7.00 C 12487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 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 B 501 " distance=2.05 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.05 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.07 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.02 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.04 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.05 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS G 501 " distance=2.06 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS I 501 " distance=2.05 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.02 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.09 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.04 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 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=2.09 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.04 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA b 3 " - " MAN b 4 " " BMA j 3 " - " MAN j 4 " ALPHA1-6 " BMA P 3 " - " MAN P 5 " " BMA j 3 " - " MAN j 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " 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 Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 618 " " NAG A 703 " - " ASN A 637 " " NAG B 601 " - " ASN B 88 " " NAG B 614 " - " ASN B 295 " " NAG B 620 " - " ASN B 339 " " NAG B 621 " - " ASN B 355 " " NAG C 703 " - " ASN C 618 " " NAG C 704 " - " ASN C 637 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 615 " - " ASN G 295 " " NAG G 620 " - " ASN G 339 " " NAG G 621 " - " ASN G 355 " " NAG G 622 " - " ASN G 392 " " NAG G 627 " - " ASN G 448 " " NAG I 601 " - " ASN I 88 " " NAG I 619 " - " ASN I 295 " " NAG I 625 " - " ASN I 339 " " NAG I 626 " - " ASN I 355 " " NAG I 631 " - " ASN I 448 " " NAG M 1 " - " ASN B 160 " " NAG N 1 " - " ASN B 197 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 262 " " NAG Q 1 " - " ASN B 301 " " NAG R 1 " - " ASN B 332 " " NAG S 1 " - " ASN B 386 " " NAG T 1 " - " ASN B 448 " " NAG U 1 " - " ASN B 392 " " NAG V 1 " - " ASN B 276 " " NAG W 1 " - " ASN C 611 " " NAG X 1 " - " ASN G 88 " " NAG Y 1 " - " ASN G 160 " " NAG Z 1 " - " ASN G 197 " " NAG a 1 " - " ASN G 234 " " NAG b 1 " - " ASN G 262 " " NAG c 1 " - " ASN G 301 " " NAG d 1 " - " ASN G 332 " " NAG e 1 " - " ASN G 279 " " NAG f 1 " - " ASN G 386 " " NAG g 1 " - " ASN I 160 " " NAG h 1 " - " ASN I 197 " " NAG i 1 " - " ASN I 234 " " NAG j 1 " - " ASN I 262 " " NAG k 1 " - " ASN I 279 " " NAG l 1 " - " ASN I 301 " " NAG m 1 " - " ASN I 332 " " NAG n 1 " - " ASN I 386 " " NAG o 1 " - " ASN I 392 " Time building additional restraints: 9.38 Conformation dependent library (CDL) restraints added in 2.6 seconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4422 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 43 sheets defined 16.8% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 537 through 543 removed outlier: 3.666A pdb=" N ALA A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 595 removed outlier: 3.579A pdb=" N VAL A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASP A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 removed outlier: 3.611A pdb=" N ILE A 622 " --> pdb=" O ASN A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 632 removed outlier: 3.502A pdb=" N ASP A 632 " --> pdb=" O TRP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 648 removed outlier: 3.696A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 661 Processing helix chain 'B' and resid 99 through 116 removed outlier: 3.782A pdb=" N ILE B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.602A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 481 removed outlier: 4.208A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 537 through 546 removed outlier: 3.695A pdb=" N ALA C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER C 546 " --> pdb=" O ARG C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 595 removed outlier: 3.641A pdb=" N VAL C 580 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASP C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 632 removed outlier: 3.618A pdb=" N ASP C 632 " --> pdb=" O TRP C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 649 removed outlier: 4.967A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU C 648 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 661 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.760A pdb=" N SER D 31 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER D 32 " --> pdb=" O ILE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'E' and resid 26 through 29 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 543 removed outlier: 3.764A pdb=" N ALA F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 595 removed outlier: 4.415A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASP F 589 " --> pdb=" O HIS F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 removed outlier: 3.595A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 632 Processing helix chain 'F' and resid 638 through 648 removed outlier: 4.451A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 652 through 661 Processing helix chain 'G' and resid 99 through 116 removed outlier: 3.641A pdb=" N GLN G 103 " --> pdb=" O ASN G 99 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.634A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 481 removed outlier: 3.722A pdb=" N ARG G 480 " --> pdb=" O ARG G 476 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 476 through 481' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.761A pdb=" N SER H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER H 32 " --> pdb=" O ILE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'I' and resid 99 through 116 removed outlier: 3.618A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU I 116 " --> pdb=" O TRP I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 350 Processing helix chain 'I' and resid 351 through 353 No H-bonds generated for 'chain 'I' and resid 351 through 353' Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.557A pdb=" N THR I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 481 removed outlier: 3.830A pdb=" N ARG I 480 " --> pdb=" O ARG I 476 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.760A pdb=" N SER J 31 " --> pdb=" O SER J 28 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER J 32 " --> pdb=" O ILE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'K' and resid 26 through 29 Processing helix chain 'L' and resid 26 through 29 Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 46 removed outlier: 9.153A pdb=" N ILE B 491 " --> pdb=" O PRO B 43 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TRP B 45 " --> pdb=" O VAL B 489 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N VAL B 489 " --> pdb=" O TRP B 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 75 through 76 removed outlier: 4.360A pdb=" N VAL B 75 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 172 through 176 removed outlier: 3.734A pdb=" N VAL B 172 " --> pdb=" O PHE B 159 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 159 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS B 131 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS B 189 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU B 190 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.249A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 259 through 261 removed outlier: 4.130A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B 292 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 271 through 273 removed outlier: 3.511A pdb=" N ILE B 271 " --> pdb=" O GLN B 287 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU B 452 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 304 through 307 removed outlier: 3.903A pdb=" N LYS B 305 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 329 through 334 removed outlier: 3.785A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 6 through 8 removed outlier: 3.621A pdb=" N GLY D 8 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR D 21 " --> pdb=" O GLY D 8 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 17 through 18 removed outlier: 3.884A pdb=" N THR D 69 " --> pdb=" O LYS D 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 47 through 49 removed outlier: 4.514A pdb=" N TRP D 37 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 19 through 24 removed outlier: 4.042A pdb=" N VAL E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 90 through 92 removed outlier: 3.644A pdb=" N ALA E 95B" --> pdb=" O ASP E 92 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 35 through 46 removed outlier: 3.540A pdb=" N GLY G 495 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N ILE G 491 " --> pdb=" O PRO G 43 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N TRP G 45 " --> pdb=" O VAL G 489 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N VAL G 489 " --> pdb=" O TRP G 45 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 75 through 76 removed outlier: 4.458A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 92 through 94 removed outlier: 4.142A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 169 through 176 removed outlier: 3.923A pdb=" N VAL G 172 " --> pdb=" O PHE G 159 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE G 159 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS G 131 " --> pdb=" O LYS G 189 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS G 189 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.269A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'G' and resid 256 through 257 Processing sheet with id=AC2, first strand: chain 'G' and resid 259 through 260 removed outlier: 3.728A pdb=" N LEU G 452 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 259 through 260 removed outlier: 6.589A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 383 through 385 removed outlier: 3.756A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 383 through 385 removed outlier: 3.756A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR G 297 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN G 295 " --> pdb=" O ASN G 332 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 304 through 307 removed outlier: 3.576A pdb=" N LYS G 305 " --> pdb=" O TYR G 319 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 6 through 8 removed outlier: 3.620A pdb=" N GLY H 8 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR H 21 " --> pdb=" O GLY H 8 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 17 through 18 removed outlier: 3.884A pdb=" N THR H 69 " --> pdb=" O LYS H 82 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 47 through 49 removed outlier: 4.514A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 35 through 46 removed outlier: 9.239A pdb=" N ILE I 491 " --> pdb=" O PRO I 43 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N TRP I 45 " --> pdb=" O VAL I 489 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N VAL I 489 " --> pdb=" O TRP I 45 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 53 through 55 removed outlier: 5.853A pdb=" N ILE I 215 " --> pdb=" O GLY I 250 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY I 250 " --> pdb=" O ILE I 215 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR I 217 " --> pdb=" O THR I 248 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 92 through 94 removed outlier: 4.139A pdb=" N GLY I 237 " --> pdb=" O PHE I 93 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 169 through 176 removed outlier: 3.840A pdb=" N PHE I 159 " --> pdb=" O VAL I 172 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS I 131 " --> pdb=" O LYS I 189 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS I 189 " --> pdb=" O CYS I 131 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 202 through 203 removed outlier: 5.852A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.823A pdb=" N ILE I 271 " --> pdb=" O GLN I 287 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 383 through 385 removed outlier: 3.673A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 383 through 385 removed outlier: 3.673A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR I 297 " --> pdb=" O HIS I 330 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N SER I 334 " --> pdb=" O GLN I 293 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLN I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL I 292 " --> pdb=" O ILE I 449 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 301 through 308 removed outlier: 7.656A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS I 305 " --> pdb=" O TYR I 319 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 6 through 8 removed outlier: 3.620A pdb=" N GLY J 8 " --> pdb=" O THR J 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR J 21 " --> pdb=" O GLY J 8 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 17 through 18 removed outlier: 3.884A pdb=" N THR J 69 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 47 through 49 removed outlier: 4.513A pdb=" N TRP J 37 " --> pdb=" O ILE J 49 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.042A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 90 through 92 removed outlier: 3.646A pdb=" N ALA K 95B" --> pdb=" O ASP K 92 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 19 through 24 removed outlier: 4.042A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 90 through 92 removed outlier: 3.645A pdb=" N ALA L 95B" --> pdb=" O ASP L 92 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1239 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: 5.72 Time building geometry restraints manager: 9.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 3206 1.31 - 1.45: 6838 1.45 - 1.59: 10176 1.59 - 1.73: 1 1.73 - 1.87: 150 Bond restraints: 20371 Sorted by residual: bond pdb=" C4 NAG e 1 " pdb=" O4 NAG e 1 " ideal model delta sigma weight residual 1.409 1.524 -0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" C7 NAG B 614 " pdb=" N2 NAG B 614 " ideal model delta sigma weight residual 1.346 1.243 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C1 NAG B 614 " pdb=" C2 NAG B 614 " ideal model delta sigma weight residual 1.532 1.434 0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C2 NAG B 614 " pdb=" N2 NAG B 614 " ideal model delta sigma weight residual 1.439 1.342 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C3 NAG B 614 " pdb=" C4 NAG B 614 " ideal model delta sigma weight residual 1.524 1.432 0.092 2.00e-02 2.50e+03 2.12e+01 ... (remaining 20366 not shown) Histogram of bond angle deviations from ideal: 84.34 - 95.58: 13 95.58 - 106.83: 853 106.83 - 118.07: 15448 118.07 - 129.32: 11137 129.32 - 140.56: 223 Bond angle restraints: 27674 Sorted by residual: angle pdb=" CA ASN G 448 " pdb=" C ASN G 448 " pdb=" O ASN G 448 " ideal model delta sigma weight residual 119.32 104.70 14.62 1.19e+00 7.06e-01 1.51e+02 angle pdb=" C ASN G 448 " pdb=" N ILE G 449 " pdb=" CA ILE G 449 " ideal model delta sigma weight residual 121.97 140.56 -18.59 1.80e+00 3.09e-01 1.07e+02 angle pdb=" O SER G 447 " pdb=" C SER G 447 " pdb=" N ASN G 448 " ideal model delta sigma weight residual 123.10 133.55 -10.45 1.15e+00 7.56e-01 8.26e+01 angle pdb=" C3 NAG C 704 " pdb=" C2 NAG C 704 " pdb=" N2 NAG C 704 " ideal model delta sigma weight residual 110.74 84.34 26.40 3.00e+00 1.11e-01 7.75e+01 angle pdb=" C1 NAG j 1 " pdb=" C2 NAG j 1 " pdb=" N2 NAG j 1 " ideal model delta sigma weight residual 110.79 88.76 22.03 3.00e+00 1.11e-01 5.39e+01 ... (remaining 27669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 10376 17.78 - 35.56: 781 35.56 - 53.33: 191 53.33 - 71.11: 18 71.11 - 88.89: 19 Dihedral angle restraints: 11385 sinusoidal: 4515 harmonic: 6870 Sorted by residual: dihedral pdb=" CB CYS F 605 " pdb=" SG CYS F 605 " pdb=" SG CYS I 501 " pdb=" CB CYS I 501 " ideal model delta sinusoidal sigma weight residual -86.00 2.89 -88.89 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CA GLN K 34 " pdb=" C GLN K 34 " pdb=" N TRP K 35 " pdb=" CA TRP K 35 " ideal model delta harmonic sigma weight residual 180.00 134.99 45.01 0 5.00e+00 4.00e-02 8.10e+01 dihedral pdb=" CA GLN L 34 " pdb=" C GLN L 34 " pdb=" N TRP L 35 " pdb=" CA TRP L 35 " ideal model delta harmonic sigma weight residual 180.00 135.03 44.97 0 5.00e+00 4.00e-02 8.09e+01 ... (remaining 11382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.241: 3307 0.241 - 0.483: 73 0.483 - 0.724: 5 0.724 - 0.965: 2 0.965 - 1.207: 4 Chirality restraints: 3391 Sorted by residual: chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.81 0.41 2.00e-02 2.50e+03 4.13e+02 chirality pdb=" C1 BMA V 3 " pdb=" O4 NAG V 2 " pdb=" C2 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.72 0.32 2.00e-02 2.50e+03 2.63e+02 chirality pdb=" C1 NAG j 2 " pdb=" O4 NAG j 1 " pdb=" C2 NAG j 2 " pdb=" O5 NAG j 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-02 2.50e+03 2.54e+02 ... (remaining 3388 not shown) Planarity restraints: 3440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 1 " -0.366 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG f 1 " 0.096 2.00e-02 2.50e+03 pdb=" C8 NAG f 1 " -0.192 2.00e-02 2.50e+03 pdb=" N2 NAG f 1 " 0.533 2.00e-02 2.50e+03 pdb=" O7 NAG f 1 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG U 2 " 0.344 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG U 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG U 2 " 0.100 2.00e-02 2.50e+03 pdb=" N2 NAG U 2 " -0.529 2.00e-02 2.50e+03 pdb=" O7 NAG U 2 " 0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 1 " -0.336 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG j 1 " 0.120 2.00e-02 2.50e+03 pdb=" C8 NAG j 1 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG j 1 " 0.499 2.00e-02 2.50e+03 pdb=" O7 NAG j 1 " -0.104 2.00e-02 2.50e+03 ... (remaining 3437 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 15 2.21 - 2.88: 7971 2.88 - 3.56: 27575 3.56 - 4.23: 44211 4.23 - 4.90: 67651 Nonbonded interactions: 147423 Sorted by model distance: nonbonded pdb=" CE2 PHE B 391 " pdb=" CG PRO B 470 " model vdw 1.539 3.740 nonbonded pdb=" CE3 TRP G 96 " pdb=" OE2 GLU G 275 " model vdw 1.863 3.340 nonbonded pdb=" CE2 PHE B 391 " pdb=" CB PRO B 470 " model vdw 1.868 3.740 nonbonded pdb=" O4 NAG C 704 " pdb=" O6 NAG C 704 " model vdw 1.983 2.440 nonbonded pdb=" O4 NAG A 703 " pdb=" O6 NAG A 703 " model vdw 1.998 2.440 ... (remaining 147418 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 518 through 664 or resid 701 through 702)) selection = chain 'C' selection = (chain 'F' and (resid 518 through 664 or resid 701 through 702)) } ncs_group { reference = chain 'B' selection = (chain 'G' and (resid 31 through 505 or resid 615 through 622)) selection = (chain 'I' and (resid 31 through 505 or resid 601 through 626)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'l' selection = chain 'n' selection = chain 'o' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'V' selection = chain 'Y' selection = chain 'Z' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'm' } ncs_group { reference = chain 'P' selection = chain 'j' } 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.470 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 50.340 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.330 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 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 : 0.010 0.115 20371 Z= 0.593 Angle : 1.622 26.404 27674 Z= 0.817 Chirality : 0.099 1.207 3391 Planarity : 0.015 0.306 3389 Dihedral : 13.275 79.327 6873 Min Nonbonded Distance : 1.539 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.43 % Allowed : 15.83 % Favored : 83.74 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 1.59 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.88 (0.14), residues: 2343 helix: -3.44 (0.19), residues: 333 sheet: -2.48 (0.19), residues: 564 loop : -3.71 (0.14), residues: 1446 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 896 time to evaluate : 2.198 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 outliers start: 22 outliers final: 9 residues processed: 909 average time/residue: 0.3212 time to fit residues: 439.0349 Evaluate side-chains 543 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 534 time to evaluate : 2.379 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1852 time to fit residues: 6.2875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.0770 chunk 177 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 212 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 GLN ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 656 ASN E 17 GLN ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 ASN G 170 GLN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 ASN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 ASN I 156 GLN I 170 GLN I 302 ASN ** I 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 425 ASN K 17 GLN L 17 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 20371 Z= 0.233 Angle : 0.975 12.521 27674 Z= 0.464 Chirality : 0.060 0.613 3391 Planarity : 0.006 0.055 3389 Dihedral : 8.032 39.425 2544 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.18 % Favored : 88.73 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.15), residues: 2343 helix: -2.57 (0.22), residues: 336 sheet: -1.79 (0.23), residues: 429 loop : -3.54 (0.13), residues: 1578 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 739 time to evaluate : 2.411 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 outliers start: 7 outliers final: 1 residues processed: 742 average time/residue: 0.3078 time to fit residues: 354.5664 Evaluate side-chains 539 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 538 time to evaluate : 2.157 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1754 time to fit residues: 3.1518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 176 optimal weight: 0.0970 chunk 144 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 212 optimal weight: 0.6980 chunk 229 optimal weight: 0.7980 chunk 189 optimal weight: 9.9990 chunk 211 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 170 optimal weight: 0.0980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 GLN ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN G 156 GLN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 GLN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 ASN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 348 GLN I 425 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 20371 Z= 0.203 Angle : 0.890 11.804 27674 Z= 0.422 Chirality : 0.056 0.542 3391 Planarity : 0.005 0.061 3389 Dihedral : 7.296 41.359 2544 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.55 % Favored : 87.37 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.62 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.15), residues: 2343 helix: -2.21 (0.23), residues: 339 sheet: -1.51 (0.22), residues: 504 loop : -3.43 (0.14), residues: 1500 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 683 time to evaluate : 2.271 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 outliers start: 6 outliers final: 1 residues processed: 689 average time/residue: 0.2982 time to fit residues: 319.4488 Evaluate side-chains 524 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 523 time to evaluate : 2.442 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1913 time to fit residues: 3.7726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 chunk 110 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 142 optimal weight: 0.0040 chunk 213 optimal weight: 0.0970 chunk 226 optimal weight: 4.9990 chunk 111 optimal weight: 0.0670 chunk 202 optimal weight: 6.9990 chunk 60 optimal weight: 0.4980 overall best weight: 0.1728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN B 156 GLN ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN G 99 ASN G 170 GLN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 425 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6179 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 20371 Z= 0.190 Angle : 0.852 12.594 27674 Z= 0.401 Chirality : 0.054 0.477 3391 Planarity : 0.005 0.047 3389 Dihedral : 6.842 39.830 2544 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.95 % Favored : 87.96 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.16), residues: 2343 helix: -1.91 (0.25), residues: 327 sheet: -1.45 (0.22), residues: 510 loop : -3.29 (0.14), residues: 1506 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 670 time to evaluate : 2.506 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 outliers start: 4 outliers final: 1 residues processed: 672 average time/residue: 0.2978 time to fit residues: 313.6708 Evaluate side-chains 504 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 503 time to evaluate : 2.117 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2251 time to fit residues: 3.1986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 168 optimal weight: 0.0980 chunk 93 optimal weight: 3.9990 chunk 193 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 203 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN B 195 ASN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 GLN ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 ASN H 78 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 20371 Z= 0.339 Angle : 0.943 11.549 27674 Z= 0.451 Chirality : 0.055 0.421 3391 Planarity : 0.005 0.060 3389 Dihedral : 6.974 41.023 2544 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.85 % Favored : 85.02 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.15), residues: 2343 helix: -1.75 (0.24), residues: 351 sheet: -1.54 (0.23), residues: 489 loop : -3.39 (0.14), residues: 1503 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 638 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 640 average time/residue: 0.2977 time to fit residues: 296.9090 Evaluate side-chains 485 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 485 time to evaluate : 2.359 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 5.9990 chunk 203 optimal weight: 0.0030 chunk 44 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 226 optimal weight: 3.9990 chunk 187 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN F 540 GLN F 656 ASN G 99 ASN G 258 GLN ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 20371 Z= 0.214 Angle : 0.842 10.459 27674 Z= 0.397 Chirality : 0.053 0.416 3391 Planarity : 0.004 0.047 3389 Dihedral : 6.596 39.989 2544 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.59 % Favored : 87.32 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.16), residues: 2343 helix: -1.60 (0.25), residues: 354 sheet: -1.43 (0.23), residues: 474 loop : -3.21 (0.14), residues: 1515 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 631 time to evaluate : 2.348 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 outliers start: 0 outliers final: 0 residues processed: 631 average time/residue: 0.2857 time to fit residues: 283.6119 Evaluate side-chains 483 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 483 time to evaluate : 2.235 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 chunk 165 optimal weight: 0.0670 chunk 190 optimal weight: 0.5980 chunk 126 optimal weight: 0.5980 chunk 225 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 GLN ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN ** F 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN I 170 GLN I 195 ASN I 276 ASN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 20371 Z= 0.186 Angle : 0.830 10.064 27674 Z= 0.390 Chirality : 0.052 0.458 3391 Planarity : 0.004 0.048 3389 Dihedral : 6.397 42.308 2544 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.06 % Favored : 86.81 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.55 (0.16), residues: 2343 helix: -1.18 (0.27), residues: 336 sheet: -1.41 (0.23), residues: 516 loop : -3.20 (0.15), residues: 1491 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 627 time to evaluate : 2.413 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 outliers start: 1 outliers final: 0 residues processed: 627 average time/residue: 0.2841 time to fit residues: 280.4048 Evaluate side-chains 488 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 488 time to evaluate : 2.256 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 177 optimal weight: 0.5980 chunk 205 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 ASN K 93 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6304 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 20371 Z= 0.217 Angle : 0.839 10.287 27674 Z= 0.396 Chirality : 0.052 0.488 3391 Planarity : 0.004 0.046 3389 Dihedral : 6.304 40.066 2544 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.10 % Favored : 86.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.51 (0.16), residues: 2343 helix: -1.04 (0.27), residues: 339 sheet: -1.33 (0.22), residues: 522 loop : -3.23 (0.15), residues: 1482 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 619 time to evaluate : 2.433 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 outliers start: 0 outliers final: 0 residues processed: 619 average time/residue: 0.2899 time to fit residues: 282.4539 Evaluate side-chains 492 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 2.247 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 9.9990 chunk 197 optimal weight: 0.7980 chunk 210 optimal weight: 10.0000 chunk 126 optimal weight: 0.1980 chunk 91 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 189 optimal weight: 10.0000 chunk 198 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN F 540 GLN G 99 ASN ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 170 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 20371 Z= 0.236 Angle : 0.856 10.221 27674 Z= 0.404 Chirality : 0.052 0.481 3391 Planarity : 0.005 0.049 3389 Dihedral : 6.346 40.113 2544 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.62 % Favored : 86.30 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.16), residues: 2343 helix: -0.80 (0.28), residues: 336 sheet: -1.30 (0.24), residues: 480 loop : -3.26 (0.14), residues: 1527 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 628 time to evaluate : 2.058 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 outliers start: 1 outliers final: 0 residues processed: 628 average time/residue: 0.2927 time to fit residues: 291.0512 Evaluate side-chains 485 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 485 time to evaluate : 2.327 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 0.0670 chunk 135 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 154 optimal weight: 6.9990 chunk 233 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 chunk 185 optimal weight: 0.2980 chunk 19 optimal weight: 0.4980 chunk 143 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN G 99 ASN ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN G 478 ASN H 78 GLN I 170 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 20371 Z= 0.193 Angle : 0.856 10.473 27674 Z= 0.401 Chirality : 0.052 0.475 3391 Planarity : 0.004 0.044 3389 Dihedral : 6.205 39.993 2544 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.16 % Favored : 87.75 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.16), residues: 2343 helix: -0.77 (0.28), residues: 333 sheet: -1.13 (0.23), residues: 510 loop : -3.25 (0.14), residues: 1500 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 626 time to evaluate : 2.423 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 outliers start: 1 outliers final: 0 residues processed: 627 average time/residue: 0.2913 time to fit residues: 287.8986 Evaluate side-chains 504 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 2.229 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 171 optimal weight: 4.9990 chunk 27 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 185 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 190 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 163 optimal weight: 0.0970 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN G 99 ASN ** G 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 GLN ** G 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.124406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.099520 restraints weight = 41175.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.102601 restraints weight = 25004.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.104721 restraints weight = 17523.367| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 20371 Z= 0.275 Angle : 0.876 10.226 27674 Z= 0.415 Chirality : 0.054 0.631 3391 Planarity : 0.005 0.047 3389 Dihedral : 6.340 39.082 2544 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.04 % Favored : 85.87 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.16), residues: 2343 helix: -0.68 (0.28), residues: 339 sheet: -1.27 (0.24), residues: 486 loop : -3.31 (0.14), residues: 1518 =============================================================================== Job complete usr+sys time: 5267.43 seconds wall clock time: 96 minutes 7.91 seconds (5767.91 seconds total)