Starting phenix.real_space_refine on Sun Feb 18 09:26:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9a_25754/02_2024/7t9a_25754_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9a_25754/02_2024/7t9a_25754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9a_25754/02_2024/7t9a_25754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9a_25754/02_2024/7t9a_25754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9a_25754/02_2024/7t9a_25754_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9a_25754/02_2024/7t9a_25754_updated.pdb" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.033 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 131 5.16 5 C 13459 2.51 5 N 3572 2.21 5 O 4355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "M GLU 1": "OE1" <-> "OE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21517 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3418 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 23, 'TRANS': 410} Chain breaks: 3 Chain: "B" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "J" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "K" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3410 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 23, 'TRANS': 409} Chain breaks: 3 Chain: "D" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "M" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "N" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "E" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3418 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 23, 'TRANS': 410} Chain breaks: 4 Chain: "F" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "O" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "P" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1052 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 799 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "T" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.74, per 1000 atoms: 0.59 Number of scatterers: 21517 At special positions: 0 Unit cell: (120.51, 129.78, 188.49, 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 131 16.00 O 4355 8.00 N 3572 7.00 C 13459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.05 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.04 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.08 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 7 " " MAN S 4 " - " MAN S 5 " " BMA Y 3 " - " MAN Y 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA S 3 " - " MAN S 4 " " MAN S 4 " - " MAN S 6 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " BETA1-6 " NAG T 1 " - " FUC T 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG U 1 " - " FUC U 2 " " NAG a 1 " - " FUC a 2 " " NAG b 1 " - " FUC b 2 " " NAG h 1 " - " FUC h 2 " " NAG i 1 " - " FUC i 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 137 " " NAG A 604 " - " ASN A 355 " " NAG A 605 " - " ASN A 276 " " NAG A 606 " - " ASN A 392 " " NAG A 607 " - " ASN A 339 " " NAG A 608 " - " ASN A 295 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 301 " " NAG A 611 " - " ASN A 197 " " NAG A 612 " - " ASN A 133 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 625 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 137 " " NAG C 604 " - " ASN C 355 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 448 " " NAG C 610 " - " ASN C 301 " " NAG C 611 " - " ASN C 197 " " NAG C 612 " - " ASN C 133 " " NAG D 701 " - " ASN D 625 " " NAG D 702 " - " ASN D 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 137 " " NAG E 604 " - " ASN E 355 " " NAG E 605 " - " ASN E 276 " " NAG E 606 " - " ASN E 392 " " NAG E 607 " - " ASN E 339 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 301 " " NAG E 611 " - " ASN E 197 " " NAG E 612 " - " ASN E 133 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 625 " " NAG G 1 " - " ASN A 386 " " NAG I 1 " - " ASN A 332 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 156 " " NAG S 1 " - " ASN A 160 " " NAG T 1 " - " ASN B 618 " " NAG U 1 " - " ASN B 611 " " NAG V 1 " - " ASN C 160 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 332 " " NAG Y 1 " - " ASN C 262 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN D 618 " " NAG b 1 " - " ASN D 611 " " NAG c 1 " - " ASN E 386 " " NAG d 1 " - " ASN E 332 " " NAG e 1 " - " ASN E 262 " " NAG f 1 " - " ASN E 156 " " NAG g 1 " - " ASN E 160 " " NAG h 1 " - " ASN F 618 " " NAG i 1 " - " ASN F 611 " Time building additional restraints: 9.24 Conformation dependent library (CDL) restraints added in 3.6 seconds 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 53 sheets defined 17.0% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.35 Creating SS restraints... Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.750A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 150 No H-bonds generated for 'chain 'A' and resid 140 through 150' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 335 through 351 removed outlier: 4.072A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 475 through 485 removed outlier: 3.588A pdb=" N SER A 481 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N TYR A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 525 removed outlier: 4.401A pdb=" N GLY B 525 " --> pdb=" O GLY B 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 522 through 525' Processing helix chain 'B' and resid 528 through 541 removed outlier: 5.305A pdb=" N MET B 533 " --> pdb=" O GLY B 529 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU B 535 " --> pdb=" O ALA B 531 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR B 536 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL B 537 " --> pdb=" O MET B 533 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 595 Processing helix chain 'B' and resid 619 through 622 No H-bonds generated for 'chain 'B' and resid 619 through 622' Processing helix chain 'B' and resid 628 through 634 Processing helix chain 'B' and resid 639 through 661 removed outlier: 3.674A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 31 No H-bonds generated for 'chain 'J' and resid 29 through 31' Processing helix chain 'J' and resid 61 through 63 No H-bonds generated for 'chain 'J' and resid 61 through 63' Processing helix chain 'J' and resid 84 through 86 No H-bonds generated for 'chain 'J' and resid 84 through 86' Processing helix chain 'K' and resid 80 through 82 No H-bonds generated for 'chain 'K' and resid 80 through 82' Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.727A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 150 No H-bonds generated for 'chain 'C' and resid 140 through 150' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 335 through 351 removed outlier: 4.021A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 475 through 485 removed outlier: 5.046A pdb=" N TYR C 484 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS C 485 " --> pdb=" O GLU C 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 525 removed outlier: 4.382A pdb=" N GLY D 525 " --> pdb=" O GLY D 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 522 through 525' Processing helix chain 'D' and resid 528 through 541 removed outlier: 5.364A pdb=" N MET D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU D 535 " --> pdb=" O ALA D 531 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N THR D 536 " --> pdb=" O SER D 532 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL D 537 " --> pdb=" O MET D 533 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN D 541 " --> pdb=" O VAL D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 595 Processing helix chain 'D' and resid 619 through 622 No H-bonds generated for 'chain 'D' and resid 619 through 622' Processing helix chain 'D' and resid 628 through 634 Processing helix chain 'D' and resid 640 through 661 Processing helix chain 'M' and resid 29 through 31 No H-bonds generated for 'chain 'M' and resid 29 through 31' Processing helix chain 'M' and resid 61 through 63 No H-bonds generated for 'chain 'M' and resid 61 through 63' Processing helix chain 'M' and resid 84 through 86 No H-bonds generated for 'chain 'M' and resid 84 through 86' Processing helix chain 'N' and resid 80 through 82 No H-bonds generated for 'chain 'N' and resid 80 through 82' Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.742A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 150 No H-bonds generated for 'chain 'E' and resid 140 through 150' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'E' and resid 335 through 351 removed outlier: 4.005A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 476 through 485 removed outlier: 3.962A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LYS E 485 " --> pdb=" O SER E 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 528 through 541 removed outlier: 5.185A pdb=" N MET F 533 " --> pdb=" O GLY F 529 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR F 534 " --> pdb=" O ALA F 530 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU F 535 " --> pdb=" O ALA F 531 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR F 536 " --> pdb=" O SER F 532 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL F 537 " --> pdb=" O MET F 533 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN F 541 " --> pdb=" O VAL F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 595 Processing helix chain 'F' and resid 619 through 622 No H-bonds generated for 'chain 'F' and resid 619 through 622' Processing helix chain 'F' and resid 628 through 632 Processing helix chain 'F' and resid 636 through 661 removed outlier: 3.784A pdb=" N THR F 639 " --> pdb=" O SER F 636 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLN F 640 " --> pdb=" O ASN F 637 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE F 641 " --> pdb=" O TYR F 638 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 31 No H-bonds generated for 'chain 'O' and resid 29 through 31' Processing helix chain 'O' and resid 61 through 63 No H-bonds generated for 'chain 'O' and resid 61 through 63' Processing helix chain 'O' and resid 84 through 86 No H-bonds generated for 'chain 'O' and resid 84 through 86' Processing helix chain 'P' and resid 80 through 82 No H-bonds generated for 'chain 'P' and resid 80 through 82' Processing helix chain 'H' and resid 52B through 53 No H-bonds generated for 'chain 'H' and resid 52B through 53' Processing helix chain 'H' and resid 61 through 63 No H-bonds generated for 'chain 'H' and resid 61 through 63' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.712A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= D, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= E, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= F, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.768A pdb=" N ALA A 433 " --> pdb=" O THR A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 271 through 273 Processing sheet with id= H, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.347A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 301 through 308 removed outlier: 4.144A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 5.891A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 3 through 6 Processing sheet with id= K, first strand: chain 'J' and resid 107 through 109 removed outlier: 5.936A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'J' and resid 93 through 95 Processing sheet with id= M, first strand: chain 'K' and resid 19 through 24 Processing sheet with id= N, first strand: chain 'K' and resid 102 through 104 removed outlier: 3.504A pdb=" N ALA K 84 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'K' and resid 89 through 91 Processing sheet with id= P, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= Q, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.589A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= S, first strand: chain 'C' and resid 91 through 94 Processing sheet with id= T, first strand: chain 'C' and resid 130 through 133 Processing sheet with id= U, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= V, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.664A pdb=" N ALA C 433 " --> pdb=" O THR C 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'C' and resid 271 through 274 Processing sheet with id= X, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.354A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 301 through 308 removed outlier: 4.015A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 5.928A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 3 through 6 Processing sheet with id= AA, first strand: chain 'M' and resid 107 through 109 removed outlier: 5.921A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'M' and resid 93 through 95 Processing sheet with id= AC, first strand: chain 'N' and resid 19 through 24 Processing sheet with id= AD, first strand: chain 'N' and resid 102 through 104 removed outlier: 3.538A pdb=" N ALA N 84 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'N' and resid 89 through 91 Processing sheet with id= AF, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= AG, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.522A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR E 244 " --> pdb=" O ILE E 84 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= AI, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.522A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'E' and resid 130 through 133 Processing sheet with id= AK, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= AL, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.774A pdb=" N ALA E 433 " --> pdb=" O THR E 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'E' and resid 271 through 274 Processing sheet with id= AN, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.312A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'E' and resid 301 through 308 removed outlier: 3.750A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 5.994A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'O' and resid 3 through 6 Processing sheet with id= AQ, first strand: chain 'O' and resid 107 through 109 removed outlier: 5.911A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'O' and resid 93 through 95 Processing sheet with id= AS, first strand: chain 'P' and resid 19 through 24 Processing sheet with id= AT, first strand: chain 'P' and resid 102 through 104 removed outlier: 6.105A pdb=" N GLN P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU P 46 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'P' and resid 89 through 91 Processing sheet with id= AV, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= AW, first strand: chain 'H' and resid 107 through 109 removed outlier: 5.800A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'H' and resid 93 through 100 Processing sheet with id= AY, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= AZ, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.582A pdb=" N LYS L 103 " --> pdb=" O LEU L 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= AZ Processing sheet with id= BA, first strand: chain 'L' and resid 85 through 90 removed outlier: 5.968A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) 708 hydrogen bonds defined for protein. 1836 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: 8.21 Time building geometry restraints manager: 9.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.42: 9029 1.42 - 1.66: 12747 1.66 - 1.90: 175 1.90 - 2.14: 0 2.14 - 2.38: 1 Bond restraints: 21952 Sorted by residual: bond pdb=" C SER L 94 " pdb=" N PHE L 96 " ideal model delta sigma weight residual 1.333 2.382 -1.049 1.28e-02 6.10e+03 6.72e+03 bond pdb=" CB ASP K 27B" pdb=" CG ASP K 27B" ideal model delta sigma weight residual 1.516 1.351 0.165 2.50e-02 1.60e+03 4.34e+01 bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.398 -0.072 1.10e-02 8.26e+03 4.33e+01 bond pdb=" CB LEU L 33 " pdb=" CG LEU L 33 " ideal model delta sigma weight residual 1.530 1.656 -0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" CB LEU K 107 " pdb=" CG LEU K 107 " ideal model delta sigma weight residual 1.530 1.652 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 21947 not shown) Histogram of bond angle deviations from ideal: 97.36 - 104.78: 405 104.78 - 112.19: 10693 112.19 - 119.61: 8685 119.61 - 127.02: 9712 127.02 - 134.43: 311 Bond angle restraints: 29806 Sorted by residual: angle pdb=" C SER L 94 " pdb=" N PHE L 96 " pdb=" CA PHE L 96 " ideal model delta sigma weight residual 122.05 102.01 20.04 1.48e+00 4.57e-01 1.83e+02 angle pdb=" O SER L 94 " pdb=" C SER L 94 " pdb=" N PHE L 96 " ideal model delta sigma weight residual 123.34 110.98 12.36 1.37e+00 5.33e-01 8.14e+01 angle pdb=" CA SER L 94 " pdb=" C SER L 94 " pdb=" N PHE L 96 " ideal model delta sigma weight residual 116.50 127.89 -11.39 1.44e+00 4.82e-01 6.26e+01 angle pdb=" C CYS C 239 " pdb=" N PRO C 240 " pdb=" CA PRO C 240 " ideal model delta sigma weight residual 119.56 126.77 -7.21 1.01e+00 9.80e-01 5.10e+01 angle pdb=" C GLU E 492 " pdb=" N PRO E 493 " pdb=" CA PRO E 493 " ideal model delta sigma weight residual 119.87 127.12 -7.25 1.04e+00 9.25e-01 4.86e+01 ... (remaining 29801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.68: 13649 21.68 - 43.37: 405 43.37 - 65.05: 143 65.05 - 86.74: 55 86.74 - 108.42: 23 Dihedral angle restraints: 14275 sinusoidal: 6843 harmonic: 7432 Sorted by residual: dihedral pdb=" CA THR E 77 " pdb=" C THR E 77 " pdb=" N ASP E 78 " pdb=" CA ASP E 78 " ideal model delta harmonic sigma weight residual -180.00 -151.57 -28.43 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ASP C 78 " pdb=" C ASP C 78 " pdb=" N PRO C 79 " pdb=" CA PRO C 79 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA ASN E 94 " pdb=" C ASN E 94 " pdb=" N MET E 95 " pdb=" CA MET E 95 " ideal model delta harmonic sigma weight residual 180.00 155.94 24.06 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 14272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.264: 3347 0.264 - 0.528: 248 0.528 - 0.792: 3 0.792 - 1.056: 2 1.056 - 1.320: 1 Chirality restraints: 3601 Sorted by residual: chirality pdb=" C1 FUC b 2 " pdb=" O6 NAG b 1 " pdb=" C2 FUC b 2 " pdb=" O5 FUC b 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.08 -1.32 2.00e-02 2.50e+03 4.36e+03 chirality pdb=" C1 MAN S 6 " pdb=" O6 MAN S 4 " pdb=" C2 MAN S 6 " pdb=" O5 MAN S 6 " both_signs ideal model delta sigma weight residual False 2.40 1.73 0.67 2.00e-02 2.50e+03 1.13e+03 chirality pdb=" C1 MAN S 5 " pdb=" O3 MAN S 4 " pdb=" C2 MAN S 5 " pdb=" O5 MAN S 5 " both_signs ideal model delta sigma weight residual False 2.40 1.91 0.49 2.00e-02 2.50e+03 5.91e+02 ... (remaining 3598 not shown) Planarity restraints: 3736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG g 1 " 0.327 2.00e-02 2.50e+03 2.78e-01 9.67e+02 pdb=" C7 NAG g 1 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG g 1 " 0.174 2.00e-02 2.50e+03 pdb=" N2 NAG g 1 " -0.488 2.00e-02 2.50e+03 pdb=" O7 NAG g 1 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " -0.326 2.00e-02 2.50e+03 2.77e-01 9.61e+02 pdb=" C7 NAG R 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " -0.175 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " 0.486 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 701 " 0.312 2.00e-02 2.50e+03 2.72e-01 9.27e+02 pdb=" C7 NAG D 701 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG D 701 " 0.125 2.00e-02 2.50e+03 pdb=" N2 NAG D 701 " -0.489 2.00e-02 2.50e+03 pdb=" O7 NAG D 701 " 0.120 2.00e-02 2.50e+03 ... (remaining 3733 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 6167 2.83 - 3.35: 18625 3.35 - 3.87: 35977 3.87 - 4.38: 42926 4.38 - 4.90: 69265 Nonbonded interactions: 172960 Sorted by model distance: nonbonded pdb=" O5 NAG T 1 " pdb=" O6 NAG T 1 " model vdw 2.315 2.432 nonbonded pdb=" N ASP M 84 " pdb=" OD1 ASP M 84 " model vdw 2.372 2.520 nonbonded pdb=" N ASP J 84 " pdb=" OD1 ASP J 84 " model vdw 2.373 2.520 nonbonded pdb=" N ASP O 84 " pdb=" OD1 ASP O 84 " model vdw 2.375 2.520 nonbonded pdb=" O5 NAG R 2 " pdb=" O6 NAG R 2 " model vdw 2.383 2.432 ... (remaining 172955 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 57 or resid 68 through 503 or resid 601 through \ 612)) selection = chain 'C' selection = (chain 'E' and (resid 33 through 57 or resid 68 through 503 or resid 601 through \ 612)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'b' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'h' and resid 1) selection = (chain 'i' and resid 1) } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'K' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'Y' selection = chain 'e' } 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: 2.100 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: 10.090 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 61.390 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.220 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 : 0.022 1.049 21952 Z= 1.386 Angle : 1.738 20.039 29806 Z= 1.142 Chirality : 0.133 1.320 3601 Planarity : 0.016 0.278 3673 Dihedral : 13.070 108.419 9401 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.71 % Allowed : 3.59 % Favored : 95.70 % Rotamer: Outliers : 2.68 % Allowed : 1.74 % Favored : 95.58 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.16), residues: 2536 helix: -0.21 (0.25), residues: 375 sheet: 0.91 (0.18), residues: 800 loop : 0.04 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.007 TRP A 96 HIS 0.009 0.002 HIS F 585 PHE 0.036 0.006 PHE L 98 TYR 0.052 0.006 TYR N 96 ARG 0.013 0.001 ARG O 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 318 time to evaluate : 2.654 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: A 108 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8704 (mp) REVERT: A 215 ILE cc_start: 0.9239 (mt) cc_final: 0.9033 (pt) REVERT: J 28 THR cc_start: 0.8600 (m) cc_final: 0.8348 (p) REVERT: K 94 ARG cc_start: 0.6261 (OUTLIER) cc_final: 0.5631 (tpt170) REVERT: M 3 GLN cc_start: 0.8305 (mt0) cc_final: 0.7990 (mt0) REVERT: N 26 THR cc_start: 0.8860 (t) cc_final: 0.8257 (t) REVERT: N 94 ARG cc_start: 0.5883 (mpt180) cc_final: 0.3607 (mmt180) REVERT: E 69 TRP cc_start: 0.7257 (OUTLIER) cc_final: 0.6103 (m100) REVERT: E 95 MET cc_start: 0.9054 (ptm) cc_final: 0.8767 (ptm) REVERT: E 137 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7783 (m-40) REVERT: F 635 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8704 (pp) REVERT: O 6 GLU cc_start: 0.7865 (mp0) cc_final: 0.7509 (mp0) REVERT: P 94 ARG cc_start: 0.5913 (OUTLIER) cc_final: 0.4032 (tpp-160) REVERT: H 29 PHE cc_start: 0.5122 (m-10) cc_final: 0.4652 (m-10) REVERT: H 43 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8542 (pttt) REVERT: H 78 LEU cc_start: 0.7352 (tp) cc_final: 0.6917 (tp) REVERT: H 82 MET cc_start: 0.7848 (mtm) cc_final: 0.7631 (mpp) REVERT: L 5 THR cc_start: 0.8802 (p) cc_final: 0.8519 (m) REVERT: L 37 GLN cc_start: 0.6040 (tt0) cc_final: 0.5679 (tt0) REVERT: L 46 LEU cc_start: 0.7230 (tp) cc_final: 0.6760 (tp) REVERT: L 70 ASP cc_start: 0.8341 (t0) cc_final: 0.8055 (t0) REVERT: L 96 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6761 (m-80) outliers start: 60 outliers final: 12 residues processed: 366 average time/residue: 0.3947 time to fit residues: 210.1956 Evaluate side-chains 172 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 153 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 169 ARG Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 96 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 214 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 199 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 230 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 82 GLN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN J 3 GLN J 13 GLN J 52 ASN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN D 577 GLN D 616 ASN D 650 GLN N 17 GLN ** H 52BASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21952 Z= 0.205 Angle : 0.665 13.202 29806 Z= 0.343 Chirality : 0.048 0.263 3601 Planarity : 0.004 0.039 3673 Dihedral : 9.233 79.537 4799 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.15 % Favored : 96.49 % Rotamer: Outliers : 2.10 % Allowed : 6.07 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.17), residues: 2538 helix: 1.24 (0.27), residues: 360 sheet: 0.62 (0.18), residues: 817 loop : -0.14 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 479 HIS 0.004 0.001 HIS A 105 PHE 0.023 0.002 PHE H 27 TYR 0.014 0.001 TYR M 100F ARG 0.007 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 191 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9003 (mtp) cc_final: 0.8755 (mtp) REVERT: K 94 ARG cc_start: 0.5937 (mpt180) cc_final: 0.4894 (mmt-90) REVERT: D 616 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7902 (t0) REVERT: D 632 ASP cc_start: 0.8591 (t70) cc_final: 0.8300 (t0) REVERT: M 11 LEU cc_start: 0.7781 (tp) cc_final: 0.7359 (mp) REVERT: N 94 ARG cc_start: 0.6000 (mpt180) cc_final: 0.3710 (mmt180) REVERT: E 69 TRP cc_start: 0.7445 (OUTLIER) cc_final: 0.6470 (m100) REVERT: E 137 ASN cc_start: 0.8004 (OUTLIER) cc_final: 0.7721 (m-40) REVERT: E 303 THR cc_start: 0.8256 (m) cc_final: 0.7634 (p) REVERT: O 6 GLU cc_start: 0.7668 (mp0) cc_final: 0.7450 (mp0) REVERT: P 94 ARG cc_start: 0.5844 (mpt180) cc_final: 0.4042 (tpp-160) REVERT: H 38 ARG cc_start: 0.8118 (ptt180) cc_final: 0.7886 (ptm160) REVERT: H 43 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8576 (pttt) REVERT: H 67 PHE cc_start: 0.6331 (m-10) cc_final: 0.5199 (m-10) REVERT: H 69 ILE cc_start: 0.0202 (mt) cc_final: -0.0038 (mt) REVERT: H 78 LEU cc_start: 0.7259 (tp) cc_final: 0.7021 (tp) REVERT: H 82 LEU cc_start: 0.6053 (pp) cc_final: 0.5466 (mp) REVERT: L 75 ILE cc_start: 0.6544 (mp) cc_final: 0.6130 (tp) outliers start: 47 outliers final: 22 residues processed: 228 average time/residue: 0.3633 time to fit residues: 125.2442 Evaluate side-chains 175 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 150 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 101 ASP Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 96 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 231 optimal weight: 30.0000 chunk 249 optimal weight: 20.0000 chunk 205 optimal weight: 3.9990 chunk 229 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 185 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 103 GLN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN D 653 GLN F 585 HIS O 39 GLN P 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 21952 Z= 0.578 Angle : 0.814 12.340 29806 Z= 0.414 Chirality : 0.052 0.320 3601 Planarity : 0.005 0.050 3673 Dihedral : 7.848 55.460 4772 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.89 % Favored : 94.84 % Rotamer: Outliers : 1.83 % Allowed : 7.68 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.16), residues: 2538 helix: 0.92 (0.27), residues: 360 sheet: 0.36 (0.18), residues: 799 loop : -0.63 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 479 HIS 0.010 0.002 HIS E 105 PHE 0.023 0.003 PHE F 520 TYR 0.017 0.002 TYR J 59 ARG 0.008 0.001 ARG E 350 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 163 time to evaluate : 2.457 Fit side-chains revert: symmetry clash REVERT: K 94 ARG cc_start: 0.6406 (mpt180) cc_final: 0.5200 (mmt180) REVERT: D 620 SER cc_start: 0.8670 (m) cc_final: 0.8350 (p) REVERT: N 94 ARG cc_start: 0.6439 (mpt180) cc_final: 0.4112 (mmt180) REVERT: E 69 TRP cc_start: 0.7767 (OUTLIER) cc_final: 0.6326 (m100) REVERT: E 95 MET cc_start: 0.8994 (ptm) cc_final: 0.8700 (ptm) REVERT: E 137 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7924 (m-40) REVERT: O 6 GLU cc_start: 0.7734 (mp0) cc_final: 0.7459 (mp0) REVERT: P 66 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7957 (tttt) REVERT: P 94 ARG cc_start: 0.5951 (mpt180) cc_final: 0.3925 (tpp-160) REVERT: P 107 LEU cc_start: 0.7228 (mp) cc_final: 0.6862 (mt) REVERT: H 38 ARG cc_start: 0.8029 (ptt180) cc_final: 0.7827 (ptm160) REVERT: H 43 LYS cc_start: 0.8822 (mmtt) cc_final: 0.8530 (pttp) REVERT: H 67 PHE cc_start: 0.6295 (m-10) cc_final: 0.4516 (m-10) REVERT: H 82 LEU cc_start: 0.5846 (pp) cc_final: 0.5307 (mp) REVERT: L 49 TYR cc_start: 0.7091 (p90) cc_final: 0.6847 (p90) REVERT: L 78 LEU cc_start: 0.6372 (mt) cc_final: 0.5888 (mp) outliers start: 41 outliers final: 30 residues processed: 196 average time/residue: 0.3557 time to fit residues: 106.9369 Evaluate side-chains 172 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain J residue 101 ASP Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 105 GLN Chi-restraints excluded: chain P residue 66 LYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 228 optimal weight: 10.0000 chunk 173 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 155 optimal weight: 7.9990 chunk 231 optimal weight: 30.0000 chunk 245 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN F 538 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21952 Z= 0.183 Angle : 0.569 11.550 29806 Z= 0.290 Chirality : 0.045 0.292 3601 Planarity : 0.004 0.055 3673 Dihedral : 6.491 56.906 4768 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.74 % Favored : 95.98 % Rotamer: Outliers : 1.34 % Allowed : 8.88 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.17), residues: 2538 helix: 1.26 (0.28), residues: 363 sheet: 0.37 (0.18), residues: 811 loop : -0.63 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP L 35 HIS 0.004 0.001 HIS A 105 PHE 0.019 0.002 PHE L 71 TYR 0.013 0.001 TYR L 49 ARG 0.004 0.000 ARG L 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9007 (mtp) cc_final: 0.8643 (mtp) REVERT: K 94 ARG cc_start: 0.6326 (mpt180) cc_final: 0.5238 (mmt180) REVERT: D 632 ASP cc_start: 0.8682 (t70) cc_final: 0.8410 (t0) REVERT: N 42 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8178 (mppt) REVERT: N 94 ARG cc_start: 0.6254 (mpt180) cc_final: 0.4065 (mmt180) REVERT: E 69 TRP cc_start: 0.7658 (OUTLIER) cc_final: 0.6238 (m100) REVERT: E 95 MET cc_start: 0.8828 (ptm) cc_final: 0.8517 (ptm) REVERT: E 137 ASN cc_start: 0.8024 (OUTLIER) cc_final: 0.7761 (m-40) REVERT: O 6 GLU cc_start: 0.7611 (mp0) cc_final: 0.7315 (mp0) REVERT: P 94 ARG cc_start: 0.5827 (mpt180) cc_final: 0.3873 (tpp-160) REVERT: P 107 LEU cc_start: 0.7054 (mp) cc_final: 0.6690 (mt) REVERT: H 38 ARG cc_start: 0.8056 (ptt180) cc_final: 0.7718 (ptm160) REVERT: H 67 PHE cc_start: 0.6362 (m-10) cc_final: 0.5122 (m-10) REVERT: H 82 LEU cc_start: 0.5836 (pp) cc_final: 0.5200 (mp) REVERT: H 100 TYR cc_start: 0.6926 (m-80) cc_final: 0.6594 (m-80) REVERT: L 49 TYR cc_start: 0.6742 (p90) cc_final: 0.6513 (p90) REVERT: L 72 THR cc_start: 0.6797 (t) cc_final: 0.6349 (p) REVERT: L 73 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7199 (pt) outliers start: 30 outliers final: 16 residues processed: 178 average time/residue: 0.3678 time to fit residues: 100.2688 Evaluate side-chains 158 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 42 LYS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 204 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 3 optimal weight: 0.0370 chunk 182 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 209 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 125 optimal weight: 0.4980 chunk 220 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN M 105 GLN N 38 GLN F 538 GLN P 17 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21952 Z= 0.177 Angle : 0.544 10.842 29806 Z= 0.276 Chirality : 0.044 0.274 3601 Planarity : 0.004 0.051 3673 Dihedral : 5.786 59.585 4764 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.90 % Favored : 95.82 % Rotamer: Outliers : 1.83 % Allowed : 8.97 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.17), residues: 2538 helix: 1.45 (0.29), residues: 363 sheet: 0.42 (0.18), residues: 809 loop : -0.69 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP L 35 HIS 0.004 0.001 HIS A 105 PHE 0.023 0.001 PHE H 29 TYR 0.013 0.001 TYR L 32 ARG 0.003 0.000 ARG O 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 152 time to evaluate : 2.611 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.9023 (mtp) cc_final: 0.8646 (mtp) REVERT: K 94 ARG cc_start: 0.6350 (mpt180) cc_final: 0.5840 (tpt170) REVERT: D 620 SER cc_start: 0.8665 (m) cc_final: 0.8379 (p) REVERT: D 632 ASP cc_start: 0.8715 (t70) cc_final: 0.8291 (t0) REVERT: N 94 ARG cc_start: 0.6412 (mpt180) cc_final: 0.4101 (mmt180) REVERT: E 69 TRP cc_start: 0.7713 (OUTLIER) cc_final: 0.6288 (m100) REVERT: E 95 MET cc_start: 0.8835 (ptm) cc_final: 0.8520 (ptm) REVERT: E 137 ASN cc_start: 0.8034 (OUTLIER) cc_final: 0.7778 (m-40) REVERT: O 6 GLU cc_start: 0.7561 (mp0) cc_final: 0.7246 (mp0) REVERT: P 94 ARG cc_start: 0.5785 (mpt180) cc_final: 0.3825 (tpp-160) REVERT: P 107 LEU cc_start: 0.6931 (mp) cc_final: 0.6529 (mt) REVERT: H 38 ARG cc_start: 0.8027 (ptt180) cc_final: 0.7749 (ptm160) REVERT: H 43 LYS cc_start: 0.8787 (mmtt) cc_final: 0.8534 (pttp) REVERT: H 67 PHE cc_start: 0.6433 (m-10) cc_final: 0.5171 (m-10) REVERT: H 82 LEU cc_start: 0.5948 (pp) cc_final: 0.5255 (mp) outliers start: 41 outliers final: 22 residues processed: 184 average time/residue: 0.3484 time to fit residues: 98.9106 Evaluate side-chains 162 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 82 optimal weight: 6.9990 chunk 221 optimal weight: 0.0470 chunk 48 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 245 optimal weight: 1.9990 chunk 204 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 20 optimal weight: 0.0670 chunk 81 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 overall best weight: 0.6016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21952 Z= 0.135 Angle : 0.515 10.481 29806 Z= 0.260 Chirality : 0.043 0.266 3601 Planarity : 0.003 0.051 3673 Dihedral : 5.355 57.031 4764 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.74 % Favored : 96.06 % Rotamer: Outliers : 0.94 % Allowed : 10.08 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), residues: 2538 helix: 1.54 (0.29), residues: 363 sheet: 0.53 (0.18), residues: 805 loop : -0.69 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP L 35 HIS 0.003 0.000 HIS A 105 PHE 0.013 0.001 PHE E 382 TYR 0.010 0.001 TYR L 36 ARG 0.005 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9035 (mtp) cc_final: 0.8639 (mtp) REVERT: J 3 GLN cc_start: 0.8516 (tp40) cc_final: 0.8305 (tp-100) REVERT: K 94 ARG cc_start: 0.6315 (mpt180) cc_final: 0.5820 (tpt170) REVERT: D 632 ASP cc_start: 0.8709 (t70) cc_final: 0.8294 (t0) REVERT: N 94 ARG cc_start: 0.6379 (mpt180) cc_final: 0.4070 (mmt180) REVERT: E 95 MET cc_start: 0.8708 (ptm) cc_final: 0.8399 (ptm) REVERT: E 137 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.7767 (m-40) REVERT: F 635 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8407 (pp) REVERT: O 6 GLU cc_start: 0.7553 (mp0) cc_final: 0.7301 (mp0) REVERT: P 47 MET cc_start: 0.7440 (mmt) cc_final: 0.7167 (mmt) REVERT: P 94 ARG cc_start: 0.5803 (mpt180) cc_final: 0.3826 (tpp-160) REVERT: P 107 LEU cc_start: 0.6592 (mp) cc_final: 0.6179 (mt) REVERT: H 38 ARG cc_start: 0.8057 (ptt180) cc_final: 0.7734 (ptm160) REVERT: H 67 PHE cc_start: 0.6472 (m-10) cc_final: 0.5290 (m-10) REVERT: H 82 LEU cc_start: 0.5854 (pp) cc_final: 0.5178 (mp) outliers start: 21 outliers final: 16 residues processed: 169 average time/residue: 0.3616 time to fit residues: 93.4857 Evaluate side-chains 155 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 236 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 140 optimal weight: 0.0470 chunk 179 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 244 optimal weight: 30.0000 chunk 153 optimal weight: 0.9990 chunk 149 optimal weight: 0.0970 chunk 113 optimal weight: 1.9990 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 399 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21952 Z= 0.166 Angle : 0.517 10.341 29806 Z= 0.261 Chirality : 0.043 0.264 3601 Planarity : 0.004 0.049 3673 Dihedral : 5.168 52.444 4761 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.94 % Favored : 95.86 % Rotamer: Outliers : 1.38 % Allowed : 9.82 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.17), residues: 2538 helix: 1.49 (0.29), residues: 368 sheet: 0.54 (0.18), residues: 809 loop : -0.72 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP L 35 HIS 0.004 0.001 HIS A 105 PHE 0.020 0.001 PHE H 29 TYR 0.012 0.001 TYR L 49 ARG 0.008 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 94 ARG cc_start: 0.6351 (mpt180) cc_final: 0.5809 (tpt170) REVERT: D 632 ASP cc_start: 0.8745 (t70) cc_final: 0.8330 (t0) REVERT: N 94 ARG cc_start: 0.6420 (mpt180) cc_final: 0.4071 (mmt180) REVERT: E 95 MET cc_start: 0.8764 (ptm) cc_final: 0.8448 (ptm) REVERT: E 137 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7838 (m-40) REVERT: F 635 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8363 (pp) REVERT: O 3 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7322 (mm110) REVERT: P 94 ARG cc_start: 0.5796 (mpt180) cc_final: 0.3808 (tpp-160) REVERT: P 107 LEU cc_start: 0.6588 (mp) cc_final: 0.6165 (mt) REVERT: H 38 ARG cc_start: 0.7981 (ptt180) cc_final: 0.7634 (ptm160) REVERT: H 67 PHE cc_start: 0.6477 (m-10) cc_final: 0.5220 (m-10) REVERT: H 82 LEU cc_start: 0.5865 (pp) cc_final: 0.5162 (mp) outliers start: 31 outliers final: 17 residues processed: 169 average time/residue: 0.3702 time to fit residues: 96.3681 Evaluate side-chains 154 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 78 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 151 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 146 optimal weight: 0.0870 chunk 73 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 overall best weight: 2.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21952 Z= 0.318 Angle : 0.593 10.669 29806 Z= 0.297 Chirality : 0.045 0.280 3601 Planarity : 0.004 0.050 3673 Dihedral : 5.441 48.844 4761 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.04 % Favored : 94.80 % Rotamer: Outliers : 1.29 % Allowed : 10.35 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2538 helix: 1.47 (0.29), residues: 363 sheet: 0.36 (0.18), residues: 822 loop : -0.79 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP L 35 HIS 0.006 0.001 HIS E 105 PHE 0.015 0.002 PHE E 53 TYR 0.012 0.001 TYR L 49 ARG 0.005 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 75 LYS cc_start: 0.9242 (mmmt) cc_final: 0.8970 (mmmm) REVERT: K 94 ARG cc_start: 0.6325 (mpt180) cc_final: 0.5919 (tpt170) REVERT: D 632 ASP cc_start: 0.8835 (t70) cc_final: 0.8401 (t0) REVERT: N 94 ARG cc_start: 0.6540 (mpt180) cc_final: 0.4040 (mmt180) REVERT: E 95 MET cc_start: 0.8938 (ptm) cc_final: 0.8627 (ptm) REVERT: E 137 ASN cc_start: 0.8052 (OUTLIER) cc_final: 0.7822 (m-40) REVERT: F 635 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8344 (pp) REVERT: P 94 ARG cc_start: 0.6024 (mpt180) cc_final: 0.3956 (tpp-160) REVERT: P 107 LEU cc_start: 0.6749 (mp) cc_final: 0.6283 (mt) REVERT: H 38 ARG cc_start: 0.7934 (ptt180) cc_final: 0.7560 (ptm160) REVERT: H 67 PHE cc_start: 0.6531 (m-10) cc_final: 0.5314 (m-10) REVERT: H 82 LEU cc_start: 0.5672 (pp) cc_final: 0.5083 (mp) outliers start: 29 outliers final: 21 residues processed: 158 average time/residue: 0.3570 time to fit residues: 86.9396 Evaluate side-chains 156 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 78 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 222 optimal weight: 0.0980 chunk 234 optimal weight: 20.0000 chunk 213 optimal weight: 0.9990 chunk 228 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 179 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 chunk 215 optimal weight: 0.0060 chunk 227 optimal weight: 5.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21952 Z= 0.162 Angle : 0.528 10.459 29806 Z= 0.266 Chirality : 0.043 0.268 3601 Planarity : 0.003 0.049 3673 Dihedral : 5.146 52.934 4760 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.41 % Favored : 95.47 % Rotamer: Outliers : 1.03 % Allowed : 10.58 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.17), residues: 2538 helix: 1.54 (0.29), residues: 362 sheet: 0.40 (0.18), residues: 810 loop : -0.78 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP L 35 HIS 0.003 0.001 HIS A 105 PHE 0.012 0.001 PHE E 382 TYR 0.010 0.001 TYR L 36 ARG 0.004 0.000 ARG J 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 94 ARG cc_start: 0.6331 (mpt180) cc_final: 0.5908 (tpt170) REVERT: D 632 ASP cc_start: 0.8788 (t70) cc_final: 0.8348 (t0) REVERT: N 94 ARG cc_start: 0.6504 (mpt180) cc_final: 0.4627 (tpt170) REVERT: E 95 MET cc_start: 0.8785 (ptm) cc_final: 0.8467 (ptm) REVERT: E 137 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7835 (m-40) REVERT: F 635 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8310 (pp) REVERT: P 94 ARG cc_start: 0.5866 (mpt180) cc_final: 0.3853 (tpp-160) REVERT: P 107 LEU cc_start: 0.6372 (mp) cc_final: 0.6030 (mt) REVERT: H 38 ARG cc_start: 0.7939 (ptt180) cc_final: 0.7573 (ptm160) REVERT: H 67 PHE cc_start: 0.6443 (m-10) cc_final: 0.5206 (m-10) REVERT: H 82 LEU cc_start: 0.5650 (pp) cc_final: 0.5076 (mp) outliers start: 23 outliers final: 16 residues processed: 153 average time/residue: 0.3738 time to fit residues: 87.5727 Evaluate side-chains 149 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 32 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 149 optimal weight: 8.9990 chunk 241 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 167 optimal weight: 0.3980 chunk 253 optimal weight: 2.9990 chunk 232 optimal weight: 0.4980 chunk 201 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21952 Z= 0.160 Angle : 0.520 10.303 29806 Z= 0.261 Chirality : 0.043 0.264 3601 Planarity : 0.003 0.049 3673 Dihedral : 4.962 52.832 4760 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.73 % Favored : 95.15 % Rotamer: Outliers : 0.89 % Allowed : 10.98 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.17), residues: 2538 helix: 1.62 (0.29), residues: 362 sheet: 0.49 (0.19), residues: 792 loop : -0.79 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP L 35 HIS 0.003 0.001 HIS A 105 PHE 0.012 0.001 PHE E 382 TYR 0.021 0.001 TYR L 49 ARG 0.003 0.000 ARG H 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 3 GLN cc_start: 0.8347 (tp40) cc_final: 0.8083 (tp-100) REVERT: J 105 GLN cc_start: 0.8201 (mp10) cc_final: 0.7972 (mp10) REVERT: K 94 ARG cc_start: 0.6427 (mpt180) cc_final: 0.5864 (tpt170) REVERT: D 632 ASP cc_start: 0.8792 (t70) cc_final: 0.8353 (t0) REVERT: N 94 ARG cc_start: 0.6510 (mpt180) cc_final: 0.4624 (tpt170) REVERT: E 137 ASN cc_start: 0.8057 (OUTLIER) cc_final: 0.7814 (m-40) REVERT: E 150 MET cc_start: 0.8302 (mmm) cc_final: 0.7393 (mpp) REVERT: F 635 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8277 (pp) REVERT: P 94 ARG cc_start: 0.5800 (mpt180) cc_final: 0.3792 (tpp-160) REVERT: P 107 LEU cc_start: 0.6545 (mp) cc_final: 0.6189 (mt) REVERT: H 38 ARG cc_start: 0.7924 (ptt180) cc_final: 0.7482 (ptm160) REVERT: H 43 LYS cc_start: 0.8937 (mmtt) cc_final: 0.8651 (pttt) REVERT: H 67 PHE cc_start: 0.6474 (m-10) cc_final: 0.5231 (m-10) REVERT: H 82 LEU cc_start: 0.5713 (pp) cc_final: 0.5068 (mp) outliers start: 20 outliers final: 16 residues processed: 155 average time/residue: 0.3633 time to fit residues: 85.7754 Evaluate side-chains 147 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 160 optimal weight: 4.9990 chunk 214 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.0370 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.076655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.057849 restraints weight = 65222.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.059741 restraints weight = 36508.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.060918 restraints weight = 25681.227| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21952 Z= 0.142 Angle : 0.514 10.214 29806 Z= 0.258 Chirality : 0.043 0.263 3601 Planarity : 0.003 0.049 3673 Dihedral : 4.835 54.053 4760 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.33 % Favored : 95.55 % Rotamer: Outliers : 0.71 % Allowed : 11.11 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.17), residues: 2538 helix: 1.67 (0.29), residues: 362 sheet: 0.57 (0.19), residues: 813 loop : -0.84 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP L 35 HIS 0.003 0.001 HIS A 105 PHE 0.012 0.001 PHE L 71 TYR 0.010 0.001 TYR L 36 ARG 0.004 0.000 ARG H 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3538.83 seconds wall clock time: 66 minutes 19.84 seconds (3979.84 seconds total)