Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 13:11:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orq_20178/04_2023/6orq_20178.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orq_20178/04_2023/6orq_20178.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/6orq_20178/04_2023/6orq_20178.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orq_20178/04_2023/6orq_20178.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orq_20178/04_2023/6orq_20178.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6orq_20178/04_2023/6orq_20178.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= -0.000 sd= 0.144 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 132 5.16 5 C 12626 2.51 5 N 3364 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 PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 456": "NH1" <-> "NH2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 94": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 327": "NH1" <-> "NH2" Residue "G ARG 456": "NH1" <-> "NH2" Residue "G ARG 469": "NH1" <-> "NH2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 94": "NH1" <-> "NH2" Residue "I PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 327": "NH1" <-> "NH2" Residue "I ARG 456": "NH1" <-> "NH2" Residue "I ARG 469": "NH1" <-> "NH2" Residue "J ARG 38": "NH1" <-> "NH2" Residue "J ARG 66": "NH1" <-> "NH2" Residue "J TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 94": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K ARG 61": "NH1" <-> "NH2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 20176 Number of models: 1 Model: "" Number of chains: 40 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: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3573 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 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: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} 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: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3573 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "I" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3573 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "J" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "K" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "L" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} 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: 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: "P" 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: 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: "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: 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: "g" 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: "h" 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" 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: "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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 10.89, per 1000 atoms: 0.54 Number of scatterers: 20176 At special positions: 0 Unit cell: (146.472, 145.036, 162.268, 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 132 16.00 O 4054 8.00 N 3364 7.00 C 12626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.05 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.07 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.05 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.06 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.04 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.04 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=2.06 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.04 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA d 3 " - " MAN d 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 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 602 " - " ASN B 160 " " NAG B 615 " - " ASN B 295 " " NAG B 616 " - " ASN B 301 " " NAG B 619 " - " ASN B 339 " " NAG B 620 " - " ASN B 355 " " NAG B 623 " - " ASN B 392 " " NAG B 624 " - " ASN B 448 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 618 " " NAG C 703 " - " ASN C 637 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 601 " - " ASN G 88 " " NAG G 611 " - " ASN G 295 " " NAG G 617 " - " ASN G 339 " " NAG G 618 " - " ASN G 355 " " NAG G 621 " - " ASN G 392 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 160 " " NAG I 614 " - " ASN I 295 " " NAG I 615 " - " ASN I 301 " " NAG I 619 " - " ASN I 339 " " NAG I 620 " - " ASN I 355 " " NAG I 623 " - " ASN I 392 " " NAG M 1 " - " ASN B 197 " " NAG N 1 " - " ASN B 234 " " NAG O 1 " - " ASN B 262 " " NAG P 1 " - " ASN B 279 " " NAG Q 1 " - " ASN B 332 " " NAG R 1 " - " ASN B 386 " " NAG S 1 " - " ASN G 160 " " NAG T 1 " - " ASN G 234 " " NAG U 1 " - " ASN G 262 " " NAG V 1 " - " ASN G 279 " " NAG W 1 " - " ASN G 301 " " NAG X 1 " - " ASN G 332 " " NAG Y 1 " - " ASN G 386 " " NAG Z 1 " - " ASN G 448 " " NAG a 1 " - " ASN G 197 " " NAG b 1 " - " ASN I 197 " " NAG c 1 " - " ASN I 234 " " NAG d 1 " - " ASN I 262 " " NAG e 1 " - " ASN I 279 " " NAG f 1 " - " ASN I 332 " " NAG g 1 " - " ASN I 386 " " NAG h 1 " - " ASN I 448 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.10 Conformation dependent library (CDL) restraints added in 3.0 seconds 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 51 sheets defined 20.0% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 529 through 535 removed outlier: 3.743A pdb=" N MET A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 Processing helix chain 'A' and resid 572 through 595 removed outlier: 3.965A pdb=" N ASP A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A 590 " --> pdb=" O TYR A 586 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 624 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.998A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 652 removed outlier: 3.737A pdb=" N GLY A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 648 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 657 Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'B' and resid 59 through 64 removed outlier: 3.757A pdb=" N THR B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 99 through 117 removed outlier: 3.876A pdb=" N ILE B 108 " --> pdb=" O MET B 104 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 139 removed outlier: 3.536A pdb=" N ASN B 137 " --> pdb=" O TYR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 334 through 351 removed outlier: 3.513A pdb=" N LYS B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.997A pdb=" N VAL B 371 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.668A pdb=" N GLN B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 483 removed outlier: 3.771A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 535 removed outlier: 3.743A pdb=" N MET C 535 " --> pdb=" O GLY C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 543 Processing helix chain 'C' and resid 572 through 595 removed outlier: 3.966A pdb=" N ASP C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C 590 " --> pdb=" O TYR C 586 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN C 591 " --> pdb=" O LEU C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 624 Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.998A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU C 634 " --> pdb=" O GLN C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 652 removed outlier: 3.737A pdb=" N GLY C 644 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C 648 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 657 Processing helix chain 'C' and resid 657 through 662 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.816A pdb=" N ALA E 83 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 removed outlier: 3.742A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 Processing helix chain 'F' and resid 572 through 595 removed outlier: 3.966A pdb=" N ASP F 589 " --> pdb=" O HIS F 585 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN F 590 " --> pdb=" O TYR F 586 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN F 591 " --> pdb=" O LEU F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 624 Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.998A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 652 removed outlier: 3.737A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 652 through 657 Processing helix chain 'F' and resid 657 through 662 Processing helix chain 'G' and resid 59 through 64 removed outlier: 3.908A pdb=" N THR G 63 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 99 through 117 removed outlier: 3.616A pdb=" N ILE G 108 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 139 removed outlier: 3.554A pdb=" N ASN G 137 " --> pdb=" O TYR G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 334 through 350 removed outlier: 3.522A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 354 removed outlier: 4.280A pdb=" N GLY G 354 " --> pdb=" O LYS G 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 351 through 354' Processing helix chain 'G' and resid 368 through 373 removed outlier: 4.087A pdb=" N THR G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.570A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 425 through 429' Processing helix chain 'G' and resid 475 through 483 removed outlier: 3.940A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 64 removed outlier: 3.796A pdb=" N THR I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 67 No H-bonds generated for 'chain 'I' and resid 65 through 67' Processing helix chain 'I' and resid 99 through 117 removed outlier: 3.777A pdb=" N ILE I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN I 114 " --> pdb=" O SER I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 139 removed outlier: 3.552A pdb=" N ASN I 137 " --> pdb=" O TYR I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 334 through 350 removed outlier: 3.503A pdb=" N LYS I 347 " --> pdb=" O GLY I 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 354 removed outlier: 4.259A pdb=" N GLY I 354 " --> pdb=" O LYS I 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 351 through 354' Processing helix chain 'I' and resid 368 through 372 removed outlier: 4.028A pdb=" N VAL I 371 " --> pdb=" O ASP I 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 390 Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.726A pdb=" N GLN I 428 " --> pdb=" O ASN I 425 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG I 429 " --> pdb=" O MET I 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 425 through 429' Processing helix chain 'I' and resid 475 through 481 removed outlier: 3.974A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.816A pdb=" N ALA K 83 " --> pdb=" O GLU K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.817A pdb=" N ALA L 83 " --> pdb=" O GLU L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 3.877A pdb=" N CYS A 604 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 38 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR A 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL B 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP B 35 " --> pdb=" O THR B 499 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 46 removed outlier: 3.818A pdb=" N LYS B 490 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS B 487 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AA5, first strand: chain 'B' and resid 130 through 131 removed outlier: 4.046A pdb=" N GLN B 130 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER B 158 " --> pdb=" O GLN B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AA7, first strand: chain 'B' and resid 182 through 183 Processing sheet with id=AA8, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.582A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 259 through 261 removed outlier: 4.097A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 452 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 286 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 259 through 261 removed outlier: 4.097A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B 292 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 295 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 297 " --> pdb=" O HIS B 330 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N HIS B 330 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE B 376 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 305 through 308 removed outlier: 3.533A pdb=" N LYS B 305 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 394 through 395 removed outlier: 3.601A pdb=" N ILE B 359 " --> pdb=" O TRP B 395 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 603 through 609 removed outlier: 3.949A pdb=" N CYS C 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL G 38 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR C 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL G 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 21 Processing sheet with id=AB6, first strand: chain 'D' and resid 48 through 49 removed outlier: 3.621A pdb=" N ALA D 93 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 37 " --> pdb=" O TYR D 91 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 46 Processing sheet with id=AB8, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AB9, first strand: chain 'E' and resid 63 through 64 removed outlier: 3.973A pdb=" N SER E 63 " --> pdb=" O ASN E 74 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN E 74 " --> pdb=" O SER E 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 603 through 609 removed outlier: 3.908A pdb=" N CYS F 604 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL I 38 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR F 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL I 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.524A pdb=" N LYS G 46 " --> pdb=" O LYS G 490 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS G 490 " --> pdb=" O LYS G 46 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS G 487 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'G' and resid 92 through 93 Processing sheet with id=AC5, first strand: chain 'G' and resid 130 through 132 removed outlier: 4.057A pdb=" N GLN G 130 " --> pdb=" O SER G 158 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER G 158 " --> pdb=" O GLN G 130 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR G 132 " --> pdb=" O GLN G 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AC7, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AC8, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.706A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 271 through 274 Processing sheet with id=AD1, first strand: chain 'G' and resid 374 through 378 removed outlier: 3.731A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR G 297 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN G 295 " --> pdb=" O ASN G 332 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 304 through 308 removed outlier: 3.678A pdb=" N LYS G 305 " --> pdb=" O TYR G 319 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 394 through 395 removed outlier: 3.597A pdb=" N ILE G 359 " --> pdb=" O TRP G 395 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AD5, first strand: chain 'H' and resid 48 through 49 removed outlier: 3.621A pdb=" N ALA H 93 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 45 through 46 removed outlier: 3.737A pdb=" N LYS I 490 " --> pdb=" O LYS I 46 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 53 through 55 removed outlier: 3.790A pdb=" N HIS I 216 " --> pdb=" O ALA I 55 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 91 through 93 removed outlier: 4.087A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 121 through 122 removed outlier: 3.947A pdb=" N LEU I 122 " --> pdb=" O ILE I 201 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE I 201 " --> pdb=" O LEU I 122 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 130 through 132 removed outlier: 4.110A pdb=" N GLN I 130 " --> pdb=" O SER I 158 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER I 158 " --> pdb=" O GLN I 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 160 through 162 Processing sheet with id=AE3, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AE4, first strand: chain 'I' and resid 271 through 274 removed outlier: 3.574A pdb=" N GLN I 287 " --> pdb=" O ILE I 271 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 374 through 378 removed outlier: 3.741A pdb=" N PHE I 376 " --> pdb=" O PHE I 383 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR I 297 " --> pdb=" O HIS I 330 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL I 292 " --> pdb=" O ILE I 449 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 304 through 308 removed outlier: 3.553A pdb=" N LYS I 305 " --> pdb=" O TYR I 319 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 394 through 395 removed outlier: 3.623A pdb=" N ILE I 359 " --> pdb=" O TRP I 395 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 19 through 21 Processing sheet with id=AE9, first strand: chain 'J' and resid 48 through 49 removed outlier: 3.621A pdb=" N ALA J 93 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL J 37 " --> pdb=" O TYR J 91 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 45 through 46 Processing sheet with id=AF2, first strand: chain 'K' and resid 48 through 49 Processing sheet with id=AF3, first strand: chain 'K' and resid 63 through 64 removed outlier: 3.974A pdb=" N SER K 63 " --> pdb=" O ASN K 74 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN K 74 " --> pdb=" O SER K 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'L' and resid 45 through 46 Processing sheet with id=AF5, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AF6, first strand: chain 'L' and resid 63 through 64 removed outlier: 3.974A pdb=" N SER L 63 " --> pdb=" O ASN L 74 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN L 74 " --> pdb=" O SER L 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 415 hydrogen bonds defined for protein. 1026 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: 6.26 Time building geometry restraints manager: 9.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3261 1.31 - 1.45: 5847 1.45 - 1.58: 11293 1.58 - 1.72: 0 1.72 - 1.85: 186 Bond restraints: 20587 Sorted by residual: bond pdb=" C3 NAG a 1 " pdb=" C4 NAG a 1 " ideal model delta sigma weight residual 1.524 1.449 0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C3 BMA d 3 " pdb=" O3 BMA d 3 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C4 NAG a 1 " pdb=" C5 NAG a 1 " ideal model delta sigma weight residual 1.532 1.463 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C3 NAG a 2 " pdb=" C4 NAG a 2 " ideal model delta sigma weight residual 1.524 1.455 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C7 NAG a 1 " pdb=" C8 NAG a 1 " ideal model delta sigma weight residual 1.509 1.443 0.066 2.00e-02 2.50e+03 1.07e+01 ... (remaining 20582 not shown) Histogram of bond angle deviations from ideal: 92.83 - 101.56: 54 101.56 - 110.28: 5409 110.28 - 119.01: 11754 119.01 - 127.73: 10469 127.73 - 136.46: 248 Bond angle restraints: 27934 Sorted by residual: angle pdb=" N LEU J 45 " pdb=" CA LEU J 45 " pdb=" C LEU J 45 " ideal model delta sigma weight residual 110.80 125.23 -14.43 2.13e+00 2.20e-01 4.59e+01 angle pdb=" N LEU H 45 " pdb=" CA LEU H 45 " pdb=" C LEU H 45 " ideal model delta sigma weight residual 110.80 125.22 -14.42 2.13e+00 2.20e-01 4.58e+01 angle pdb=" N LEU D 45 " pdb=" CA LEU D 45 " pdb=" C LEU D 45 " ideal model delta sigma weight residual 110.80 125.19 -14.39 2.13e+00 2.20e-01 4.57e+01 angle pdb=" C3 NAG a 1 " pdb=" C2 NAG a 1 " pdb=" N2 NAG a 1 " ideal model delta sigma weight residual 110.74 92.83 17.91 3.00e+00 1.11e-01 3.56e+01 angle pdb=" N VAL B 371 " pdb=" CA VAL B 371 " pdb=" C VAL B 371 " ideal model delta sigma weight residual 113.42 106.98 6.44 1.17e+00 7.31e-01 3.03e+01 ... (remaining 27929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.59: 10603 15.59 - 31.18: 763 31.18 - 46.77: 242 46.77 - 62.36: 48 62.36 - 77.96: 23 Dihedral angle restraints: 11679 sinusoidal: 4659 harmonic: 7020 Sorted by residual: dihedral pdb=" CA LYS J 13 " pdb=" C LYS J 13 " pdb=" N PRO J 14 " pdb=" CA PRO J 14 " ideal model delta harmonic sigma weight residual 180.00 -123.10 -56.90 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA LYS H 13 " pdb=" C LYS H 13 " pdb=" N PRO H 14 " pdb=" CA PRO H 14 " ideal model delta harmonic sigma weight residual 180.00 -123.14 -56.86 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA LYS D 13 " pdb=" C LYS D 13 " pdb=" N PRO D 14 " pdb=" CA PRO D 14 " ideal model delta harmonic sigma weight residual -180.00 -123.15 -56.85 0 5.00e+00 4.00e-02 1.29e+02 ... (remaining 11676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 3213 0.166 - 0.333: 109 0.333 - 0.499: 11 0.499 - 0.666: 0 0.666 - 0.832: 4 Chirality restraints: 3337 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.65e+02 chirality pdb=" C5 NAG a 1 " pdb=" C4 NAG a 1 " pdb=" C6 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.41 -1.58 -0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 618 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.54e+01 ... (remaining 3334 not shown) Planarity restraints: 3514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 2 " -0.404 2.00e-02 2.50e+03 3.32e-01 1.38e+03 pdb=" C7 NAG a 2 " 0.166 2.00e-02 2.50e+03 pdb=" C8 NAG a 2 " -0.243 2.00e-02 2.50e+03 pdb=" N2 NAG a 2 " 0.545 2.00e-02 2.50e+03 pdb=" O7 NAG a 2 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 1 " 0.366 2.00e-02 2.50e+03 3.15e-01 1.24e+03 pdb=" C7 NAG a 1 " -0.127 2.00e-02 2.50e+03 pdb=" C8 NAG a 1 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG a 1 " -0.545 2.00e-02 2.50e+03 pdb=" O7 NAG a 1 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 13 " 0.064 5.00e-02 4.00e+02 9.67e-02 1.50e+01 pdb=" N PRO D 14 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " 0.053 5.00e-02 4.00e+02 ... (remaining 3511 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 297 2.61 - 3.18: 17193 3.18 - 3.76: 30218 3.76 - 4.33: 37608 4.33 - 4.90: 59246 Nonbonded interactions: 144562 Sorted by model distance: nonbonded pdb=" O4 NAG a 2 " pdb=" O6 NAG a 2 " model vdw 2.039 2.440 nonbonded pdb=" O4 NAG a 1 " pdb=" O6 NAG a 1 " model vdw 2.136 2.440 nonbonded pdb=" OG1 THR J 68 " pdb=" O GLN J 81 " model vdw 2.241 2.440 nonbonded pdb=" OG1 THR H 68 " pdb=" O GLN H 81 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR D 68 " pdb=" O GLN D 81 " model vdw 2.243 2.440 ... (remaining 144557 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'F' } ncs_group { reference = (chain 'B' and (resid 31 through 505 or resid 601 through 619)) selection = chain 'G' selection = (chain 'I' and (resid 31 through 505 or resid 601 through 619)) } 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 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'h' } ncs_group { reference = chain 'O' selection = chain 'd' } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'X' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 5.580 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 52.560 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 : 0.008 0.075 20587 Z= 0.519 Angle : 1.309 17.910 27934 Z= 0.668 Chirality : 0.077 0.832 3337 Planarity : 0.011 0.332 3463 Dihedral : 12.609 77.955 7086 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.34 % Allowed : 16.29 % Favored : 83.38 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.61 % 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: -4.97 (0.13), residues: 2388 helix: -4.26 (0.15), residues: 288 sheet: -2.27 (0.23), residues: 459 loop : -3.69 (0.12), residues: 1641 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 618 time to evaluate : 2.366 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: 22 outliers final: 10 residues processed: 629 average time/residue: 0.3348 time to fit residues: 313.9143 Evaluate side-chains 407 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 397 time to evaluate : 2.575 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.1707 time to fit residues: 6.5001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 122 optimal weight: 0.4980 chunk 97 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 140 optimal weight: 8.9990 chunk 217 optimal weight: 10.0000 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 HIS A 590 GLN ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 203 GLN B 276 ASN B 440 GLN C 570 HIS C 590 GLN C 616 ASN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 HIS F 590 GLN F 616 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 293 GLN ** G 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 440 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 258 GLN I 440 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 20587 Z= 0.336 Angle : 0.923 17.452 27934 Z= 0.449 Chirality : 0.054 0.454 3337 Planarity : 0.006 0.101 3463 Dihedral : 7.881 44.015 2607 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 15.83 % Favored : 83.96 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.35 % 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: -4.44 (0.14), residues: 2388 helix: -2.19 (0.22), residues: 354 sheet: -1.71 (0.26), residues: 390 loop : -3.73 (0.12), residues: 1644 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 526 time to evaluate : 2.523 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: 8 outliers final: 5 residues processed: 533 average time/residue: 0.3028 time to fit residues: 248.6523 Evaluate side-chains 400 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 395 time to evaluate : 2.275 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1696 time to fit residues: 4.6410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 181 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 218 optimal weight: 30.0000 chunk 235 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 330 HIS ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 422 GLN G 440 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 42 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.057 20587 Z= 0.363 Angle : 0.916 15.926 27934 Z= 0.447 Chirality : 0.054 0.432 3337 Planarity : 0.006 0.089 3463 Dihedral : 7.659 40.182 2607 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.21 % Allowed : 17.34 % Favored : 82.45 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.15), residues: 2388 helix: -1.39 (0.26), residues: 351 sheet: -1.59 (0.26), residues: 411 loop : -3.69 (0.12), residues: 1626 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 491 time to evaluate : 2.400 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 outliers start: 7 outliers final: 3 residues processed: 496 average time/residue: 0.3100 time to fit residues: 234.2013 Evaluate side-chains 378 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 375 time to evaluate : 2.285 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1690 time to fit residues: 3.9727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 20.0000 chunk 164 optimal weight: 0.2980 chunk 113 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 146 optimal weight: 0.9980 chunk 219 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 203 GLN B 258 GLN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN F 616 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 422 GLN G 440 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 42 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 20587 Z= 0.306 Angle : 0.866 14.842 27934 Z= 0.423 Chirality : 0.053 0.428 3337 Planarity : 0.006 0.088 3463 Dihedral : 7.376 42.633 2607 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 17.17 % Favored : 82.71 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 4.90 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.15), residues: 2388 helix: -1.21 (0.26), residues: 354 sheet: -1.10 (0.28), residues: 372 loop : -3.69 (0.12), residues: 1662 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 496 time to evaluate : 2.329 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 outliers start: 6 outliers final: 2 residues processed: 500 average time/residue: 0.3059 time to fit residues: 236.2469 Evaluate side-chains 361 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 359 time to evaluate : 2.425 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1624 time to fit residues: 3.6707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN F 640 GLN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 HIS G 422 GLN G 440 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 42 GLN L 89 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 20587 Z= 0.299 Angle : 0.862 14.145 27934 Z= 0.420 Chirality : 0.053 0.424 3337 Planarity : 0.005 0.083 3463 Dihedral : 7.243 39.083 2607 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 18.01 % Favored : 81.83 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.15), residues: 2388 helix: -1.25 (0.26), residues: 372 sheet: -1.47 (0.26), residues: 402 loop : -3.62 (0.13), residues: 1614 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 477 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 480 average time/residue: 0.3088 time to fit residues: 229.0184 Evaluate side-chains 360 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 359 time to evaluate : 2.187 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1779 time to fit residues: 3.1942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 5.9990 chunk 208 optimal weight: 0.0770 chunk 45 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 232 optimal weight: 6.9990 chunk 192 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 121 optimal weight: 0.0770 overall best weight: 3.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 HIS F 616 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 42 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 20587 Z= 0.313 Angle : 0.876 14.329 27934 Z= 0.426 Chirality : 0.053 0.420 3337 Planarity : 0.005 0.077 3463 Dihedral : 7.207 37.160 2607 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 17.96 % Favored : 81.95 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.26 % 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: -4.02 (0.15), residues: 2388 helix: -1.26 (0.26), residues: 372 sheet: -1.26 (0.27), residues: 378 loop : -3.66 (0.13), residues: 1638 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 470 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 471 average time/residue: 0.3067 time to fit residues: 225.1113 Evaluate side-chains 353 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 2.514 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 169 optimal weight: 0.0270 chunk 131 optimal weight: 0.8980 chunk 195 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 HIS F 616 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 440 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 42 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 20587 Z= 0.220 Angle : 0.852 14.139 27934 Z= 0.415 Chirality : 0.052 0.381 3337 Planarity : 0.005 0.073 3463 Dihedral : 7.090 41.631 2607 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 16.58 % Favored : 83.25 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.15), residues: 2388 helix: -1.15 (0.26), residues: 372 sheet: -1.24 (0.27), residues: 384 loop : -3.55 (0.13), residues: 1632 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 495 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 outliers start: 3 outliers final: 0 residues processed: 495 average time/residue: 0.3171 time to fit residues: 242.3804 Evaluate side-chains 376 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 2.294 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 45 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 147 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 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 585 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 HIS F 616 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 42 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 20587 Z= 0.213 Angle : 0.841 14.359 27934 Z= 0.410 Chirality : 0.053 0.371 3337 Planarity : 0.005 0.070 3463 Dihedral : 6.909 36.778 2607 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 16.08 % Favored : 83.84 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.15), residues: 2388 helix: -1.08 (0.26), residues: 372 sheet: -1.16 (0.28), residues: 369 loop : -3.47 (0.13), residues: 1647 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 495 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 495 average time/residue: 0.2998 time to fit residues: 232.4424 Evaluate side-chains 373 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 2.206 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 7.9990 chunk 221 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 93 optimal weight: 0.0970 chunk 169 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 214 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 302 ASN C 585 HIS ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 HIS F 616 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 67 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 440 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS I 99 ASN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 42 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 20587 Z= 0.221 Angle : 0.837 14.300 27934 Z= 0.407 Chirality : 0.053 0.372 3337 Planarity : 0.005 0.067 3463 Dihedral : 6.862 40.965 2607 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 16.33 % Favored : 83.58 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.26 % 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: -3.72 (0.15), residues: 2388 helix: -1.02 (0.26), residues: 372 sheet: -1.18 (0.28), residues: 375 loop : -3.41 (0.13), residues: 1641 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 477 time to evaluate : 2.335 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: 7 outliers final: 1 residues processed: 478 average time/residue: 0.2999 time to fit residues: 224.0010 Evaluate side-chains 382 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 381 time to evaluate : 2.198 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1674 time to fit residues: 3.2265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.0060 chunk 227 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 239 optimal weight: 10.0000 chunk 220 optimal weight: 7.9990 chunk 190 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS C 585 HIS ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN G 67 ASN G 203 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 20587 Z= 0.203 Angle : 0.840 14.226 27934 Z= 0.408 Chirality : 0.053 0.440 3337 Planarity : 0.005 0.062 3463 Dihedral : 6.756 41.048 2607 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.75 % Favored : 84.17 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.16), residues: 2388 helix: -0.95 (0.27), residues: 372 sheet: -1.13 (0.28), residues: 375 loop : -3.35 (0.13), residues: 1641 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 490 time to evaluate : 2.318 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 outliers start: 5 outliers final: 0 residues processed: 491 average time/residue: 0.3353 time to fit residues: 258.3688 Evaluate side-chains 396 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 2.569 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 5.9990 chunk 202 optimal weight: 0.1980 chunk 58 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 195 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 GLN ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 HIS F 616 ASN G 67 ASN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS I 99 ASN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 42 GLN L 53 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.088737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.070671 restraints weight = 68422.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.072887 restraints weight = 37872.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.074396 restraints weight = 25356.553| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 20587 Z= 0.212 Angle : 0.834 14.307 27934 Z= 0.405 Chirality : 0.053 0.362 3337 Planarity : 0.005 0.060 3463 Dihedral : 6.697 39.891 2607 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 16.16 % Favored : 83.75 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.35 % 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: -3.57 (0.16), residues: 2388 helix: -0.86 (0.27), residues: 375 sheet: -1.15 (0.27), residues: 390 loop : -3.32 (0.13), residues: 1623 =============================================================================== Job complete usr+sys time: 4502.96 seconds wall clock time: 82 minutes 56.43 seconds (4976.43 seconds total)