Starting phenix.real_space_refine on Fri Sep 27 18:57:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t76_25735/09_2024/7t76_25735.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t76_25735/09_2024/7t76_25735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t76_25735/09_2024/7t76_25735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t76_25735/09_2024/7t76_25735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t76_25735/09_2024/7t76_25735.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t76_25735/09_2024/7t76_25735.cif" } resolution = 4.43 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= 0.003 sd= 0.093 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 106 5.16 5 C 10329 2.51 5 N 2742 2.21 5 O 3410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16587 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3494 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 2 Chain: "C" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3494 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 2 Chain: "D" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "E" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3494 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 2 Chain: "F" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "L" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 791 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1092 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} 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: "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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" 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: "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: 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: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 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: "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: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" 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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.21, per 1000 atoms: 0.56 Number of scatterers: 16587 At special positions: 0 Unit cell: (129.95, 132.25, 161, 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 106 16.00 O 3410 8.00 N 2742 7.00 C 10329 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.21 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.07 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.06 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 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=2.01 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=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.09 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.08 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.15 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.20 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.01 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.13 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=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM16499 O3 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16503 O7 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16503 O7 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16503 O7 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16499 O3 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16499 O3 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16501 O5 NAG E 607 .*. O " rejected from bonding due to valence issues. Atom "HETATM16501 O5 NAG E 607 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Links applied ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA Z 3 " - " MAN Z 6 " " BMA c 3 " - " MAN c 4 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 7 " " MAN j 4 " - " MAN j 5 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 4 " - " MAN Z 5 " " BMA c 3 " - " MAN c 5 " " BMA i 3 " - " MAN i 5 " " BMA j 3 " - " MAN j 4 " " MAN j 4 " - " MAN j 6 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 137 " " NAG A 603 " - " ASN A 355 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 133 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 295 " " NAG C 603 " - " ASN C 355 " " NAG C 604 " - " ASN C 276 " " NAG C 605 " - " ASN C 234 " " NAG C 606 " - " ASN C 301 " " NAG C 607 " - " ASN C 88 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 276 " " NAG E 603 " - " ASN E 295 " " NAG E 604 " - " ASN E 355 " " NAG E 605 " - " ASN E 462 " " NAG E 606 " - " ASN E 88 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 1 " - " ASN A 156 " " NAG I 1 " - " ASN A 160 " " NAG J 1 " - " ASN A 197 " " NAG K 1 " - " ASN A 234 " " NAG M 1 " - " ASN A 295 " " NAG N 1 " - " ASN A 301 " " NAG O 1 " - " ASN A 332 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 392 " " NAG R 1 " - " ASN A 448 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN C 197 " " NAG U 1 " - " ASN C 262 " " NAG V 1 " - " ASN C 332 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 392 " " NAG Y 1 " - " ASN C 448 " " NAG Z 1 " - " ASN C 160 " " NAG a 1 " - " ASN C 156 " " NAG b 1 " - " ASN E 197 " " NAG c 1 " - " ASN E 262 " " NAG d 1 " - " ASN E 301 " " NAG e 1 " - " ASN E 332 " " NAG f 1 " - " ASN E 386 " " NAG g 1 " - " ASN E 392 " " NAG h 1 " - " ASN E 448 " " NAG i 1 " - " ASN E 160 " " NAG j 1 " - " ASN E 156 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.11 Conformation dependent library (CDL) restraints added in 1.8 seconds 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3594 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 27 sheets defined 24.5% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.653A pdb=" N ARG A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.773A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.827A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 464 removed outlier: 3.783A pdb=" N THR C 464 " --> pdb=" O THR C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 478 Processing helix chain 'C' and resid 479 through 484 Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 536 through 541 Processing helix chain 'D' and resid 542 through 544 No H-bonds generated for 'chain 'D' and resid 542 through 544' Processing helix chain 'D' and resid 573 through 596 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 659 removed outlier: 3.802A pdb=" N GLN D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 335 through 351 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.870A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.778A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 596 Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 650 Processing helix chain 'F' and resid 650 through 661 removed outlier: 4.375A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 650 Processing helix chain 'B' and resid 650 through 658 Processing helix chain 'B' and resid 659 through 663 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100I through 100M Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 496 removed outlier: 5.698A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.862A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 5.484A pdb=" N ILE A 215 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY A 250 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR A 217 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.682A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 322 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 466 through 470 Processing sheet with id=AA9, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.432A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 177 removed outlier: 7.527A pdb=" N HIS C 190 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 215 through 218 removed outlier: 5.379A pdb=" N ILE C 215 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY C 250 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYR C 217 " --> pdb=" O THR C 248 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 298 removed outlier: 7.022A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 330 through 334 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 467 through 470 Processing sheet with id=AB6, first strand: chain 'C' and resid 301 through 312 removed outlier: 6.782A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AB8, first strand: chain 'E' and resid 494 through 496 removed outlier: 5.485A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.609A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 91 through 92 Processing sheet with id=AC3, first strand: chain 'E' and resid 181 through 183 removed outlier: 6.856A pdb=" N ARG E 169 " --> pdb=" O TYS H 100H" (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG H 100B" --> pdb=" O TYS H 100E" (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 201 through 202 Processing sheet with id=AC5, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 6.821A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323 current: chain 'E' and resid 381 through 385 removed outlier: 4.353A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 413 through 421 current: chain 'E' and resid 466 through 470 Processing sheet with id=AC6, first strand: chain 'L' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 13 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 96 through 98 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AC8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100O through 103 460 hydrogen bonds defined for protein. 1200 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: 4.56 Time building geometry restraints manager: 5.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 4817 1.34 - 1.49: 5235 1.49 - 1.64: 6711 1.64 - 1.79: 54 1.79 - 1.94: 88 Bond restraints: 16905 Sorted by residual: bond pdb=" NE1 TRP B 610 " pdb=" CE2 TRP B 610 " ideal model delta sigma weight residual 1.370 1.290 0.080 1.10e-02 8.26e+03 5.33e+01 bond pdb=" CB LEU D 663 " pdb=" CG LEU D 663 " ideal model delta sigma weight residual 1.530 1.656 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" CB LEU B 663 " pdb=" CG LEU B 663 " ideal model delta sigma weight residual 1.530 1.651 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" CA CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sigma weight residual 1.522 1.564 -0.041 7.00e-03 2.04e+04 3.47e+01 bond pdb=" CB LEU F 663 " pdb=" CG LEU F 663 " ideal model delta sigma weight residual 1.530 1.644 -0.114 2.00e-02 2.50e+03 3.25e+01 ... (remaining 16900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.78: 22907 7.78 - 15.55: 44 15.55 - 23.33: 0 23.33 - 31.11: 0 31.11 - 38.88: 11 Bond angle restraints: 22962 Sorted by residual: angle pdb=" C2 NAG E 604 " pdb=" N2 NAG E 604 " pdb=" C7 NAG E 604 " ideal model delta sigma weight residual 124.56 163.44 -38.88 3.00e+00 1.11e-01 1.68e+02 angle pdb=" C2 NAG P 1 " pdb=" N2 NAG P 1 " pdb=" C7 NAG P 1 " ideal model delta sigma weight residual 124.56 163.08 -38.52 3.00e+00 1.11e-01 1.65e+02 angle pdb=" C2 NAG D 703 " pdb=" N2 NAG D 703 " pdb=" C7 NAG D 703 " ideal model delta sigma weight residual 124.56 162.44 -37.88 3.00e+00 1.11e-01 1.59e+02 angle pdb=" C2 NAG D 701 " pdb=" N2 NAG D 701 " pdb=" C7 NAG D 701 " ideal model delta sigma weight residual 124.56 161.76 -37.20 3.00e+00 1.11e-01 1.54e+02 angle pdb=" C2 NAG D 702 " pdb=" N2 NAG D 702 " pdb=" C7 NAG D 702 " ideal model delta sigma weight residual 124.56 161.29 -36.73 3.00e+00 1.11e-01 1.50e+02 ... (remaining 22957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.84: 11033 21.84 - 43.67: 281 43.67 - 65.50: 77 65.50 - 87.34: 54 87.34 - 109.17: 25 Dihedral angle restraints: 11470 sinusoidal: 5892 harmonic: 5578 Sorted by residual: dihedral pdb=" CB CYS F 598 " pdb=" SG CYS F 598 " pdb=" SG CYS F 604 " pdb=" CB CYS F 604 " ideal model delta sinusoidal sigma weight residual -86.00 -171.83 85.83 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual -86.00 -169.76 83.76 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CB CYS D 598 " pdb=" SG CYS D 598 " pdb=" SG CYS D 604 " pdb=" CB CYS D 604 " ideal model delta sinusoidal sigma weight residual 93.00 153.96 -60.96 1 1.00e+01 1.00e-02 4.94e+01 ... (remaining 11467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2110 0.132 - 0.263: 499 0.263 - 0.395: 203 0.395 - 0.527: 66 0.527 - 0.659: 1 Chirality restraints: 2879 Sorted by residual: chirality pdb=" C1 BMA U 3 " pdb=" O4 NAG U 2 " pdb=" C2 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.99e+02 chirality pdb=" C1 BMA S 3 " pdb=" O4 NAG S 2 " pdb=" C2 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 1.93e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.85e+02 ... (remaining 2876 not shown) Planarity restraints: 2843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 1 " -0.373 2.00e-02 2.50e+03 3.18e-01 1.27e+03 pdb=" C7 NAG Z 1 " 0.092 2.00e-02 2.50e+03 pdb=" C8 NAG Z 1 " -0.066 2.00e-02 2.50e+03 pdb=" N2 NAG Z 1 " 0.557 2.00e-02 2.50e+03 pdb=" O7 NAG Z 1 " -0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 1 " 0.354 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG S 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG S 1 " 0.073 2.00e-02 2.50e+03 pdb=" N2 NAG S 1 " -0.537 2.00e-02 2.50e+03 pdb=" O7 NAG S 1 " 0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " -0.355 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG S 2 " 0.090 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " -0.162 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " -0.109 2.00e-02 2.50e+03 ... (remaining 2840 not shown) Histogram of nonbonded interaction distances: 0.53 - 1.40: 13 1.40 - 2.28: 43 2.28 - 3.15: 13738 3.15 - 4.03: 43120 4.03 - 4.90: 75419 Warning: very small nonbonded interaction distances. Nonbonded interactions: 132333 Sorted by model distance: nonbonded pdb=" C ASN E 234 " pdb=" C2 NAG E 607 " model vdw 0.530 2.960 nonbonded pdb=" CA ASN E 234 " pdb=" C3 NAG E 607 " model vdw 0.700 3.900 nonbonded pdb=" O ASN E 234 " pdb=" N2 NAG E 607 " model vdw 0.816 3.120 nonbonded pdb=" CB PHE E 233 " pdb=" O6 NAG E 607 " model vdw 0.928 3.440 nonbonded pdb=" CA ASN E 234 " pdb=" O3 NAG E 607 " model vdw 0.962 3.470 ... (remaining 132328 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 32 through 502 or resid 601 through 605)) selection = (chain 'E' and (resid 32 through 502 or resid 601 through 605)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' } ncs_group { reference = chain 'S' selection = chain 'c' selection = chain 'i' } ncs_group { reference = (chain 'Z' and (resid 1 or resid 4 through 6)) selection = (chain 'j' and (resid 2 or resid 5 through 7)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 35.930 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.300 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:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 0.157 16905 Z= 1.383 Angle : 1.969 38.881 22962 Z= 1.177 Chirality : 0.143 0.659 2879 Planarity : 0.017 0.318 2788 Dihedral : 12.894 109.174 7774 Min Nonbonded Distance : 0.530 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.38 % Favored : 96.36 % Rotamer: Outliers : 0.77 % Allowed : 1.00 % Favored : 98.23 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.19), residues: 1894 helix: -0.17 (0.24), residues: 378 sheet: 0.62 (0.22), residues: 508 loop : 0.28 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.010 TRP E 96 HIS 0.017 0.003 HIS C 249 PHE 0.032 0.006 PHE E 233 TYR 0.058 0.008 TYR C 40 ARG 0.006 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 436 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 ILE cc_start: 0.9408 (pt) cc_final: 0.9198 (mp) REVERT: A 254 VAL cc_start: 0.9515 (t) cc_final: 0.9125 (p) REVERT: A 374 HIS cc_start: 0.7329 (t-170) cc_final: 0.6929 (t-90) REVERT: C 69 TRP cc_start: 0.8404 (m-90) cc_final: 0.7707 (m-10) REVERT: C 122 LEU cc_start: 0.9362 (mt) cc_final: 0.9132 (mp) REVERT: C 136 ASN cc_start: 0.6442 (t0) cc_final: 0.6058 (m110) REVERT: D 593 LEU cc_start: 0.9350 (mt) cc_final: 0.9149 (mm) REVERT: D 610 TRP cc_start: 0.6222 (p90) cc_final: 0.5985 (p-90) REVERT: D 655 LYS cc_start: 0.9179 (mmtm) cc_final: 0.8525 (mmmm) REVERT: E 42 VAL cc_start: 0.9298 (t) cc_final: 0.9025 (p) REVERT: E 165 LEU cc_start: 0.9258 (mt) cc_final: 0.8939 (mp) REVERT: E 180 ASP cc_start: 0.8583 (m-30) cc_final: 0.8381 (m-30) REVERT: E 186 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8240 (ptm160) REVERT: E 373 THR cc_start: 0.9127 (p) cc_final: 0.8925 (p) REVERT: E 450 THR cc_start: 0.9263 (p) cc_final: 0.9044 (p) REVERT: F 538 THR cc_start: 0.8610 (p) cc_final: 0.8342 (p) REVERT: F 581 LEU cc_start: 0.9404 (tp) cc_final: 0.9204 (tt) REVERT: F 606 THR cc_start: 0.8958 (p) cc_final: 0.8590 (t) REVERT: F 607 ASN cc_start: 0.8474 (m-40) cc_final: 0.8109 (p0) REVERT: F 624 ASP cc_start: 0.8399 (m-30) cc_final: 0.7952 (t0) REVERT: F 652 GLN cc_start: 0.7896 (tp40) cc_final: 0.7634 (tp40) REVERT: B 543 ASN cc_start: 0.8074 (m-40) cc_final: 0.7841 (t0) REVERT: B 584 GLU cc_start: 0.8922 (tt0) cc_final: 0.8246 (tp30) REVERT: B 643 TYR cc_start: 0.8935 (m-10) cc_final: 0.8038 (m-10) REVERT: L 34 SER cc_start: 0.8990 (m) cc_final: 0.8773 (p) REVERT: L 39 HIS cc_start: 0.8878 (t-90) cc_final: 0.8579 (m-70) REVERT: L 50 GLU cc_start: 0.8511 (tt0) cc_final: 0.8065 (tm-30) REVERT: L 53 ASN cc_start: 0.8897 (m-40) cc_final: 0.8135 (m-40) REVERT: L 91 TYR cc_start: 0.7852 (t80) cc_final: 0.7552 (t80) REVERT: L 98 PHE cc_start: 0.8669 (m-80) cc_final: 0.8435 (m-80) REVERT: H 18 LEU cc_start: 0.8334 (tt) cc_final: 0.7591 (tt) REVERT: H 20 LEU cc_start: 0.9316 (mt) cc_final: 0.8906 (mt) REVERT: H 29 PHE cc_start: 0.8789 (t80) cc_final: 0.8174 (t80) REVERT: H 43 LYS cc_start: 0.8998 (mptt) cc_final: 0.8450 (pttp) REVERT: H 53 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7671 (p0) REVERT: H 68 THR cc_start: 0.9158 (m) cc_final: 0.8738 (t) outliers start: 13 outliers final: 2 residues processed: 448 average time/residue: 0.2888 time to fit residues: 190.5004 Evaluate side-chains 227 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 223 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS C 167 ASN C 190 HIS C 363 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN E 374 HIS F 591 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16905 Z= 0.271 Angle : 0.806 17.329 22962 Z= 0.401 Chirality : 0.053 0.717 2879 Planarity : 0.004 0.045 2788 Dihedral : 11.549 80.855 4217 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.38 % Favored : 96.46 % Rotamer: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.19), residues: 1894 helix: 0.21 (0.26), residues: 417 sheet: 0.42 (0.22), residues: 522 loop : -0.19 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 96 HIS 0.006 0.001 HIS E 249 PHE 0.038 0.002 PHE E 233 TYR 0.017 0.002 TYR E 435 ARG 0.012 0.001 ARG E 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 298 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8443 (t0) cc_final: 0.7513 (m-40) REVERT: A 107 ASP cc_start: 0.8530 (m-30) cc_final: 0.8305 (t0) REVERT: A 181 ILE cc_start: 0.9288 (pt) cc_final: 0.8896 (mm) REVERT: A 254 VAL cc_start: 0.9489 (t) cc_final: 0.9279 (p) REVERT: C 69 TRP cc_start: 0.8624 (m-90) cc_final: 0.8207 (m-10) REVERT: C 111 LEU cc_start: 0.9429 (mm) cc_final: 0.9035 (mt) REVERT: C 122 LEU cc_start: 0.9336 (mt) cc_final: 0.9092 (mm) REVERT: C 136 ASN cc_start: 0.6403 (t0) cc_final: 0.6123 (m110) REVERT: C 190 HIS cc_start: 0.8151 (OUTLIER) cc_final: 0.7917 (m90) REVERT: C 210 PHE cc_start: 0.8474 (m-80) cc_final: 0.7869 (m-10) REVERT: D 584 GLU cc_start: 0.8788 (tp30) cc_final: 0.8194 (tm-30) REVERT: D 607 ASN cc_start: 0.8399 (m110) cc_final: 0.8119 (p0) REVERT: D 648 GLU cc_start: 0.8797 (pp20) cc_final: 0.8412 (pp20) REVERT: D 657 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8701 (mp0) REVERT: E 180 ASP cc_start: 0.8528 (m-30) cc_final: 0.8139 (m-30) REVERT: F 574 LYS cc_start: 0.6981 (pttm) cc_final: 0.6380 (mmpt) REVERT: F 607 ASN cc_start: 0.8502 (m-40) cc_final: 0.8129 (p0) REVERT: F 647 GLU cc_start: 0.8113 (pt0) cc_final: 0.7642 (pt0) REVERT: B 530 MET cc_start: 0.8541 (mtp) cc_final: 0.8035 (ppp) REVERT: B 538 THR cc_start: 0.9047 (t) cc_final: 0.8740 (t) REVERT: B 584 GLU cc_start: 0.8688 (tt0) cc_final: 0.8220 (tp30) REVERT: B 643 TYR cc_start: 0.8988 (m-10) cc_final: 0.8235 (m-10) REVERT: L 73 LEU cc_start: 0.9338 (tp) cc_final: 0.9053 (tp) REVERT: L 82 ASP cc_start: 0.6274 (m-30) cc_final: 0.5972 (m-30) REVERT: L 91 TYR cc_start: 0.7772 (t80) cc_final: 0.7453 (t80) REVERT: L 104 LEU cc_start: 0.8402 (tt) cc_final: 0.7683 (tp) REVERT: H 34 MET cc_start: 0.9513 (mmp) cc_final: 0.9240 (mmm) REVERT: H 68 THR cc_start: 0.8787 (m) cc_final: 0.8552 (t) outliers start: 1 outliers final: 0 residues processed: 299 average time/residue: 0.2717 time to fit residues: 123.7740 Evaluate side-chains 189 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 171 optimal weight: 30.0000 chunk 184 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN C 190 HIS ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS F 652 GLN B 658 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16905 Z= 0.286 Angle : 0.725 11.800 22962 Z= 0.361 Chirality : 0.049 0.470 2879 Planarity : 0.005 0.156 2788 Dihedral : 9.849 69.968 4217 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.28 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.21 (0.19), residues: 1894 helix: 0.22 (0.27), residues: 396 sheet: 0.15 (0.21), residues: 563 loop : -0.37 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 479 HIS 0.014 0.002 HIS A 374 PHE 0.044 0.002 PHE E 233 TYR 0.018 0.002 TYR E 484 ARG 0.007 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8349 (m-30) cc_final: 0.7893 (p0) REVERT: A 254 VAL cc_start: 0.9621 (t) cc_final: 0.9382 (p) REVERT: A 286 VAL cc_start: 0.9428 (t) cc_final: 0.9006 (p) REVERT: A 374 HIS cc_start: 0.7570 (t-90) cc_final: 0.6927 (t-90) REVERT: C 69 TRP cc_start: 0.8704 (m-90) cc_final: 0.8198 (m-10) REVERT: C 111 LEU cc_start: 0.9386 (mm) cc_final: 0.8952 (mt) REVERT: C 122 LEU cc_start: 0.9395 (mt) cc_final: 0.9158 (mm) REVERT: C 136 ASN cc_start: 0.6793 (t0) cc_final: 0.6474 (m110) REVERT: D 574 LYS cc_start: 0.8697 (tmmt) cc_final: 0.8324 (pttt) REVERT: D 584 GLU cc_start: 0.8981 (tp30) cc_final: 0.8250 (tm-30) REVERT: D 607 ASN cc_start: 0.8457 (m110) cc_final: 0.8138 (p0) REVERT: D 648 GLU cc_start: 0.8936 (pp20) cc_final: 0.8435 (pp20) REVERT: D 657 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8524 (mp0) REVERT: E 180 ASP cc_start: 0.8585 (m-30) cc_final: 0.8095 (m-30) REVERT: F 574 LYS cc_start: 0.7803 (pttm) cc_final: 0.7384 (mmpt) REVERT: F 576 LEU cc_start: 0.8942 (mt) cc_final: 0.8292 (tt) REVERT: F 606 THR cc_start: 0.8652 (p) cc_final: 0.8367 (t) REVERT: F 607 ASN cc_start: 0.8498 (m-40) cc_final: 0.7968 (p0) REVERT: F 647 GLU cc_start: 0.8260 (pt0) cc_final: 0.7879 (pt0) REVERT: F 652 GLN cc_start: 0.7681 (tp40) cc_final: 0.7441 (tp-100) REVERT: B 530 MET cc_start: 0.8650 (mtp) cc_final: 0.8154 (ppp) REVERT: B 536 THR cc_start: 0.8969 (p) cc_final: 0.8596 (p) REVERT: B 540 GLN cc_start: 0.9216 (mm110) cc_final: 0.8011 (mt0) REVERT: B 584 GLU cc_start: 0.8758 (tt0) cc_final: 0.8404 (tp30) REVERT: B 591 GLN cc_start: 0.9309 (tp40) cc_final: 0.8934 (tp40) REVERT: B 630 GLN cc_start: 0.9241 (mt0) cc_final: 0.8637 (mt0) REVERT: B 643 TYR cc_start: 0.9107 (m-10) cc_final: 0.8540 (m-10) REVERT: L 49 TYR cc_start: 0.8783 (p90) cc_final: 0.8292 (p90) REVERT: L 53 ASN cc_start: 0.8742 (m-40) cc_final: 0.8445 (t0) REVERT: L 73 LEU cc_start: 0.9338 (tp) cc_final: 0.9029 (tp) REVERT: L 91 TYR cc_start: 0.7634 (t80) cc_final: 0.7330 (t80) REVERT: L 104 LEU cc_start: 0.8278 (tt) cc_final: 0.8040 (tp) REVERT: H 34 MET cc_start: 0.9501 (mmp) cc_final: 0.9205 (mmm) REVERT: H 68 THR cc_start: 0.8859 (m) cc_final: 0.8415 (t) REVERT: H 80 LEU cc_start: 0.9228 (tp) cc_final: 0.8959 (tp) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.2633 time to fit residues: 100.2151 Evaluate side-chains 174 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 20.0000 chunk 128 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 chunk 171 optimal weight: 30.0000 chunk 181 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN D 630 GLN B 658 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 39 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16905 Z= 0.342 Angle : 0.734 9.239 22962 Z= 0.366 Chirality : 0.050 0.448 2879 Planarity : 0.005 0.044 2788 Dihedral : 9.187 68.933 4217 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.01 % Favored : 95.93 % Rotamer: Outliers : 0.06 % Allowed : 2.18 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.58 (0.19), residues: 1894 helix: -0.09 (0.26), residues: 408 sheet: -0.12 (0.21), residues: 569 loop : -0.58 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP H 36 HIS 0.011 0.002 HIS A 374 PHE 0.033 0.002 PHE E 233 TYR 0.021 0.002 TYR E 384 ARG 0.009 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8526 (m-30) cc_final: 0.8111 (m-30) REVERT: A 374 HIS cc_start: 0.7635 (t-90) cc_final: 0.7202 (t-90) REVERT: C 69 TRP cc_start: 0.8736 (m-90) cc_final: 0.7677 (m-10) REVERT: C 136 ASN cc_start: 0.6810 (t0) cc_final: 0.6604 (m110) REVERT: D 584 GLU cc_start: 0.9007 (tp30) cc_final: 0.8356 (tm-30) REVERT: D 626 MET cc_start: 0.6972 (tmm) cc_final: 0.6104 (tmm) REVERT: D 648 GLU cc_start: 0.8924 (pp20) cc_final: 0.8563 (tm-30) REVERT: E 180 ASP cc_start: 0.8664 (m-30) cc_final: 0.8126 (m-30) REVERT: F 576 LEU cc_start: 0.8936 (mt) cc_final: 0.8315 (tt) REVERT: F 584 GLU cc_start: 0.8441 (tp30) cc_final: 0.8090 (tm-30) REVERT: F 647 GLU cc_start: 0.8314 (pt0) cc_final: 0.7974 (pt0) REVERT: F 652 GLN cc_start: 0.7967 (tp40) cc_final: 0.7731 (tp-100) REVERT: B 530 MET cc_start: 0.8847 (mtp) cc_final: 0.8362 (ppp) REVERT: B 540 GLN cc_start: 0.9270 (mm110) cc_final: 0.8126 (mt0) REVERT: B 584 GLU cc_start: 0.9001 (tt0) cc_final: 0.8258 (tp30) REVERT: B 591 GLN cc_start: 0.9338 (tp40) cc_final: 0.9020 (tp40) REVERT: L 49 TYR cc_start: 0.8801 (p90) cc_final: 0.8241 (p90) REVERT: L 53 ASN cc_start: 0.8719 (m-40) cc_final: 0.8437 (t0) REVERT: L 91 TYR cc_start: 0.7472 (t80) cc_final: 0.7172 (t80) REVERT: H 34 MET cc_start: 0.9379 (mmp) cc_final: 0.9070 (mmm) outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.2661 time to fit residues: 89.6384 Evaluate side-chains 152 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN F 591 GLN B 658 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16905 Z= 0.201 Angle : 0.633 9.288 22962 Z= 0.312 Chirality : 0.048 0.442 2879 Planarity : 0.004 0.100 2788 Dihedral : 8.610 68.246 4217 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.75 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.45 (0.19), residues: 1894 helix: 0.16 (0.27), residues: 402 sheet: -0.07 (0.21), residues: 577 loop : -0.54 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 631 HIS 0.006 0.001 HIS A 249 PHE 0.021 0.001 PHE E 233 TYR 0.012 0.001 TYR E 484 ARG 0.007 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.815 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 180 ASP cc_start: 0.8767 (m-30) cc_final: 0.8088 (m-30) REVERT: A 374 HIS cc_start: 0.7518 (t-90) cc_final: 0.6993 (t-90) REVERT: C 69 TRP cc_start: 0.8730 (m-90) cc_final: 0.7707 (m-10) REVERT: C 104 MET cc_start: 0.9261 (tmm) cc_final: 0.9005 (tmm) REVERT: C 111 LEU cc_start: 0.9374 (mm) cc_final: 0.8964 (mt) REVERT: C 116 LEU cc_start: 0.9471 (tt) cc_final: 0.9113 (mt) REVERT: D 584 GLU cc_start: 0.9010 (tp30) cc_final: 0.8346 (tm-30) REVERT: D 648 GLU cc_start: 0.8924 (pp20) cc_final: 0.8554 (tm-30) REVERT: E 95 MET cc_start: 0.8439 (mmp) cc_final: 0.8180 (mmm) REVERT: E 180 ASP cc_start: 0.8667 (m-30) cc_final: 0.8106 (m-30) REVERT: F 576 LEU cc_start: 0.8828 (mt) cc_final: 0.8232 (tt) REVERT: F 584 GLU cc_start: 0.8369 (tp30) cc_final: 0.7918 (tm-30) REVERT: F 647 GLU cc_start: 0.8262 (pt0) cc_final: 0.7898 (pt0) REVERT: F 652 GLN cc_start: 0.7922 (tp40) cc_final: 0.7282 (tp-100) REVERT: B 530 MET cc_start: 0.8655 (mtp) cc_final: 0.8252 (ppp) REVERT: B 540 GLN cc_start: 0.9190 (mm110) cc_final: 0.8062 (mt0) REVERT: B 584 GLU cc_start: 0.8911 (tt0) cc_final: 0.8183 (tp30) REVERT: L 49 TYR cc_start: 0.8736 (p90) cc_final: 0.8434 (p90) REVERT: L 53 ASN cc_start: 0.8772 (m-40) cc_final: 0.8451 (t0) REVERT: L 91 TYR cc_start: 0.7371 (t80) cc_final: 0.7127 (t80) REVERT: L 104 LEU cc_start: 0.7832 (tp) cc_final: 0.7622 (tp) REVERT: H 13 GLN cc_start: 0.8751 (mm110) cc_final: 0.8494 (mm-40) REVERT: H 20 LEU cc_start: 0.9214 (tp) cc_final: 0.8988 (tp) REVERT: H 34 MET cc_start: 0.8797 (mmt) cc_final: 0.8539 (mmm) REVERT: H 68 THR cc_start: 0.8769 (m) cc_final: 0.8440 (p) REVERT: H 80 LEU cc_start: 0.8773 (tp) cc_final: 0.8477 (tp) REVERT: H 100 ASP cc_start: 0.8856 (t0) cc_final: 0.8640 (t0) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.2496 time to fit residues: 85.1198 Evaluate side-chains 163 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 95 optimal weight: 6.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN E 85 HIS E 348 GLN E 478 ASN F 585 HIS B 575 GLN B 585 HIS ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 16905 Z= 0.441 Angle : 0.805 9.321 22962 Z= 0.400 Chirality : 0.051 0.445 2879 Planarity : 0.005 0.068 2788 Dihedral : 8.802 71.193 4217 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.60 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.83 (0.19), residues: 1894 helix: -0.07 (0.26), residues: 408 sheet: -0.45 (0.21), residues: 551 loop : -0.73 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP H 36 HIS 0.015 0.002 HIS A 374 PHE 0.021 0.002 PHE E 210 TYR 0.020 0.002 TYR E 384 ARG 0.007 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9421 (ttt) cc_final: 0.9004 (ttt) REVERT: A 180 ASP cc_start: 0.8660 (m-30) cc_final: 0.8409 (m-30) REVERT: C 104 MET cc_start: 0.9367 (tmm) cc_final: 0.9017 (tmm) REVERT: C 111 LEU cc_start: 0.9481 (mm) cc_final: 0.9060 (mt) REVERT: C 207 LYS cc_start: 0.8600 (pttt) cc_final: 0.8270 (tptt) REVERT: C 260 LEU cc_start: 0.9231 (mt) cc_final: 0.9023 (mt) REVERT: D 584 GLU cc_start: 0.9003 (tp30) cc_final: 0.8387 (tm-30) REVERT: D 648 GLU cc_start: 0.8874 (pp20) cc_final: 0.8667 (tm-30) REVERT: E 180 ASP cc_start: 0.8784 (m-30) cc_final: 0.8102 (m-30) REVERT: F 576 LEU cc_start: 0.8939 (mt) cc_final: 0.8330 (tt) REVERT: F 584 GLU cc_start: 0.8518 (tp30) cc_final: 0.8296 (tm-30) REVERT: F 591 GLN cc_start: 0.9544 (tt0) cc_final: 0.9000 (tt0) REVERT: F 647 GLU cc_start: 0.8306 (pt0) cc_final: 0.8008 (pt0) REVERT: F 652 GLN cc_start: 0.8230 (tp40) cc_final: 0.7798 (tp40) REVERT: B 530 MET cc_start: 0.8773 (mtp) cc_final: 0.8436 (ppp) REVERT: B 591 GLN cc_start: 0.9403 (tp40) cc_final: 0.9078 (tp40) REVERT: B 593 LEU cc_start: 0.9503 (mm) cc_final: 0.9254 (tp) REVERT: B 601 LYS cc_start: 0.9186 (mmtp) cc_final: 0.8932 (mmmm) REVERT: B 634 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7772 (mp0) REVERT: L 49 TYR cc_start: 0.8819 (p90) cc_final: 0.8524 (p90) REVERT: L 53 ASN cc_start: 0.8735 (m-40) cc_final: 0.8337 (t0) REVERT: L 91 TYR cc_start: 0.7386 (t80) cc_final: 0.7127 (t80) REVERT: H 13 GLN cc_start: 0.8802 (mm110) cc_final: 0.8506 (mm-40) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2654 time to fit residues: 78.5042 Evaluate side-chains 142 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 102 optimal weight: 0.4980 chunk 153 optimal weight: 0.1980 chunk 101 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 630 GLN D 656 ASN E 85 HIS E 246 GLN F 650 GLN ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16905 Z= 0.175 Angle : 0.624 9.258 22962 Z= 0.310 Chirality : 0.048 0.434 2879 Planarity : 0.004 0.054 2788 Dihedral : 8.100 71.310 4217 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.33 % Favored : 96.62 % Rotamer: Outliers : 0.06 % Allowed : 1.06 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.59 (0.19), residues: 1894 helix: -0.00 (0.26), residues: 423 sheet: -0.11 (0.21), residues: 569 loop : -0.66 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 69 HIS 0.009 0.001 HIS A 249 PHE 0.013 0.001 PHE E 233 TYR 0.015 0.001 TYR B 643 ARG 0.003 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 214 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8747 (m-30) cc_final: 0.8493 (m-30) REVERT: C 104 MET cc_start: 0.9429 (tmm) cc_final: 0.9216 (tmm) REVERT: C 111 LEU cc_start: 0.9373 (mm) cc_final: 0.8978 (mt) REVERT: C 207 LYS cc_start: 0.8587 (pttt) cc_final: 0.8262 (tptt) REVERT: D 574 LYS cc_start: 0.8830 (tmmt) cc_final: 0.8624 (pttm) REVERT: D 584 GLU cc_start: 0.9022 (tp30) cc_final: 0.8401 (tm-30) REVERT: E 180 ASP cc_start: 0.8760 (m-30) cc_final: 0.8064 (m-30) REVERT: F 576 LEU cc_start: 0.8836 (mt) cc_final: 0.8273 (tt) REVERT: F 584 GLU cc_start: 0.8274 (tp30) cc_final: 0.7902 (tm-30) REVERT: F 601 LYS cc_start: 0.9087 (tptt) cc_final: 0.8727 (tppp) REVERT: F 647 GLU cc_start: 0.8147 (pt0) cc_final: 0.7869 (pt0) REVERT: B 530 MET cc_start: 0.8713 (mtp) cc_final: 0.8332 (ppp) REVERT: H 13 GLN cc_start: 0.8808 (mm110) cc_final: 0.8492 (mm-40) REVERT: H 34 MET cc_start: 0.8884 (mmp) cc_final: 0.8543 (mmm) REVERT: H 100 ASP cc_start: 0.8787 (t0) cc_final: 0.8576 (t0) outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 0.2516 time to fit residues: 84.5117 Evaluate side-chains 161 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 108 optimal weight: 0.1980 chunk 54 optimal weight: 9.9990 chunk 35 optimal weight: 0.3980 chunk 115 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 16 optimal weight: 0.0040 chunk 142 optimal weight: 0.5980 chunk 164 optimal weight: 7.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 630 GLN E 85 HIS F 591 GLN B 575 GLN B 658 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16905 Z= 0.184 Angle : 0.619 9.393 22962 Z= 0.312 Chirality : 0.048 0.420 2879 Planarity : 0.004 0.055 2788 Dihedral : 7.733 71.334 4217 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.91 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.20), residues: 1894 helix: 0.20 (0.27), residues: 399 sheet: -0.06 (0.22), residues: 563 loop : -0.54 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 69 HIS 0.010 0.001 HIS A 374 PHE 0.026 0.001 PHE L 98 TYR 0.016 0.001 TYR H 100R ARG 0.007 0.000 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.902 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: A 180 ASP cc_start: 0.8727 (m-30) cc_final: 0.8475 (m-30) REVERT: A 374 HIS cc_start: 0.7442 (t-90) cc_final: 0.6832 (t-170) REVERT: C 53 PHE cc_start: 0.8415 (m-80) cc_final: 0.8197 (m-80) REVERT: C 111 LEU cc_start: 0.9349 (mm) cc_final: 0.8976 (mt) REVERT: C 210 PHE cc_start: 0.8855 (m-80) cc_final: 0.8475 (m-10) REVERT: D 530 MET cc_start: 0.6232 (tpp) cc_final: 0.5844 (tpp) REVERT: D 584 GLU cc_start: 0.8993 (tp30) cc_final: 0.8368 (tm-30) REVERT: D 657 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8589 (mt-10) REVERT: E 95 MET cc_start: 0.8399 (mmp) cc_final: 0.8100 (mmm) REVERT: E 180 ASP cc_start: 0.8784 (m-30) cc_final: 0.8061 (m-30) REVERT: E 479 TRP cc_start: 0.8640 (m-90) cc_final: 0.8144 (m-90) REVERT: F 535 MET cc_start: 0.8862 (mpp) cc_final: 0.8584 (mpp) REVERT: F 576 LEU cc_start: 0.8826 (mt) cc_final: 0.8248 (tt) REVERT: F 584 GLU cc_start: 0.8327 (tp30) cc_final: 0.8005 (tm-30) REVERT: F 601 LYS cc_start: 0.9047 (tptt) cc_final: 0.8703 (tppp) REVERT: F 647 GLU cc_start: 0.8074 (pt0) cc_final: 0.7840 (pt0) REVERT: B 530 MET cc_start: 0.8647 (mtp) cc_final: 0.8356 (ppp) REVERT: B 540 GLN cc_start: 0.9074 (mm110) cc_final: 0.8154 (mt0) REVERT: B 634 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7860 (mt-10) REVERT: L 104 LEU cc_start: 0.7875 (tp) cc_final: 0.7626 (tp) REVERT: H 13 GLN cc_start: 0.8820 (mm110) cc_final: 0.8511 (mm-40) REVERT: H 28 THR cc_start: 0.8603 (m) cc_final: 0.8329 (p) REVERT: H 34 MET cc_start: 0.9043 (mmp) cc_final: 0.8648 (mmm) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2525 time to fit residues: 82.0851 Evaluate side-chains 160 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 152 optimal weight: 0.7980 chunk 159 optimal weight: 0.0970 chunk 110 optimal weight: 8.9990 chunk 178 optimal weight: 2.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN E 85 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16905 Z= 0.271 Angle : 0.666 11.350 22962 Z= 0.333 Chirality : 0.048 0.405 2879 Planarity : 0.004 0.054 2788 Dihedral : 7.689 70.081 4217 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.20), residues: 1894 helix: 0.57 (0.28), residues: 372 sheet: 0.05 (0.22), residues: 532 loop : -0.63 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 69 HIS 0.012 0.002 HIS A 374 PHE 0.020 0.002 PHE E 53 TYR 0.013 0.001 TYR D 586 ARG 0.006 0.000 ARG E 172 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.8750 (m-30) cc_final: 0.8509 (m-30) REVERT: A 374 HIS cc_start: 0.7404 (t-90) cc_final: 0.7133 (t-90) REVERT: C 111 LEU cc_start: 0.9405 (mm) cc_final: 0.9012 (mt) REVERT: C 207 LYS cc_start: 0.8747 (pttt) cc_final: 0.8358 (tptt) REVERT: C 210 PHE cc_start: 0.8918 (m-80) cc_final: 0.8584 (m-10) REVERT: D 584 GLU cc_start: 0.8980 (tp30) cc_final: 0.8377 (tm-30) REVERT: D 590 GLN cc_start: 0.9186 (tp40) cc_final: 0.8830 (tp40) REVERT: E 180 ASP cc_start: 0.8729 (m-30) cc_final: 0.8040 (m-30) REVERT: E 479 TRP cc_start: 0.8741 (m-90) cc_final: 0.7709 (m-90) REVERT: F 535 MET cc_start: 0.8937 (mpp) cc_final: 0.8648 (mpp) REVERT: F 576 LEU cc_start: 0.8869 (mt) cc_final: 0.8271 (tt) REVERT: F 584 GLU cc_start: 0.8310 (tp30) cc_final: 0.8075 (tm-30) REVERT: F 591 GLN cc_start: 0.9457 (tt0) cc_final: 0.8917 (tt0) REVERT: F 601 LYS cc_start: 0.9048 (tptt) cc_final: 0.8692 (tppp) REVERT: F 625 ASN cc_start: 0.8552 (t0) cc_final: 0.8343 (t0) REVERT: F 647 GLU cc_start: 0.7922 (pt0) cc_final: 0.7691 (pt0) REVERT: B 530 MET cc_start: 0.8683 (mtp) cc_final: 0.8418 (ppp) REVERT: B 591 GLN cc_start: 0.9402 (tp40) cc_final: 0.9041 (tp40) REVERT: B 601 LYS cc_start: 0.9056 (mmtp) cc_final: 0.8766 (mmmm) REVERT: B 630 GLN cc_start: 0.8910 (mp10) cc_final: 0.8514 (pm20) REVERT: B 634 GLU cc_start: 0.8464 (mt-10) cc_final: 0.7653 (mp0) REVERT: L 53 ASN cc_start: 0.8898 (m110) cc_final: 0.8394 (m110) REVERT: L 91 TYR cc_start: 0.6963 (t80) cc_final: 0.6731 (t80) REVERT: H 13 GLN cc_start: 0.8829 (mm110) cc_final: 0.8511 (mm-40) REVERT: H 28 THR cc_start: 0.8585 (m) cc_final: 0.8337 (p) REVERT: H 34 MET cc_start: 0.9072 (mmp) cc_final: 0.8801 (mmm) REVERT: H 100 ASP cc_start: 0.8808 (t0) cc_final: 0.8596 (t0) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2705 time to fit residues: 84.0398 Evaluate side-chains 153 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 6.9990 chunk 84 optimal weight: 0.0870 chunk 124 optimal weight: 0.9990 chunk 187 optimal weight: 9.9990 chunk 172 optimal weight: 7.9990 chunk 149 optimal weight: 0.2980 chunk 15 optimal weight: 10.0000 chunk 115 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN E 85 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16905 Z= 0.196 Angle : 0.634 10.900 22962 Z= 0.319 Chirality : 0.048 0.409 2879 Planarity : 0.004 0.051 2788 Dihedral : 7.434 70.662 4217 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.06 % Allowed : 0.18 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.20), residues: 1894 helix: 0.25 (0.27), residues: 402 sheet: -0.12 (0.22), residues: 547 loop : -0.53 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 69 HIS 0.010 0.001 HIS E 85 PHE 0.018 0.001 PHE L 98 TYR 0.013 0.001 TYR L 91 ARG 0.012 0.000 ARG C 186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 203 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8722 (m-80) cc_final: 0.8274 (m-10) REVERT: A 104 MET cc_start: 0.9423 (ttt) cc_final: 0.9005 (ttt) REVERT: A 180 ASP cc_start: 0.8751 (m-30) cc_final: 0.8501 (m-30) REVERT: A 374 HIS cc_start: 0.7407 (t-90) cc_final: 0.7091 (t70) REVERT: C 100 MET cc_start: 0.8904 (mtp) cc_final: 0.8643 (mtm) REVERT: C 111 LEU cc_start: 0.9373 (mm) cc_final: 0.9015 (mt) REVERT: C 207 LYS cc_start: 0.8773 (pttt) cc_final: 0.8364 (tptt) REVERT: C 210 PHE cc_start: 0.8931 (m-80) cc_final: 0.8553 (m-10) REVERT: C 477 ASP cc_start: 0.8555 (m-30) cc_final: 0.7864 (p0) REVERT: D 530 MET cc_start: 0.7152 (tpt) cc_final: 0.6206 (tpp) REVERT: D 584 GLU cc_start: 0.8978 (tp30) cc_final: 0.8385 (tm-30) REVERT: D 590 GLN cc_start: 0.9194 (tp40) cc_final: 0.8884 (tp40) REVERT: D 657 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8416 (mt-10) REVERT: E 95 MET cc_start: 0.8378 (mmp) cc_final: 0.7998 (mmm) REVERT: E 104 MET cc_start: 0.8963 (ttp) cc_final: 0.8448 (ttp) REVERT: E 112 TRP cc_start: 0.8810 (m100) cc_final: 0.8369 (m100) REVERT: E 180 ASP cc_start: 0.8703 (m-30) cc_final: 0.7996 (m-30) REVERT: E 226 LEU cc_start: 0.9220 (mt) cc_final: 0.8997 (mt) REVERT: E 479 TRP cc_start: 0.8379 (m-90) cc_final: 0.7493 (m-90) REVERT: F 535 MET cc_start: 0.8918 (mpp) cc_final: 0.8642 (mpp) REVERT: F 576 LEU cc_start: 0.8828 (mt) cc_final: 0.8229 (tt) REVERT: F 584 GLU cc_start: 0.8279 (tp30) cc_final: 0.7986 (tm-30) REVERT: F 601 LYS cc_start: 0.9034 (tptt) cc_final: 0.8709 (tppp) REVERT: B 530 MET cc_start: 0.8663 (mtp) cc_final: 0.8194 (mtm) REVERT: B 634 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7886 (mt-10) REVERT: L 47 MET cc_start: 0.8392 (mmp) cc_final: 0.8164 (mmm) REVERT: L 53 ASN cc_start: 0.8898 (m110) cc_final: 0.8632 (m110) REVERT: L 75 ILE cc_start: 0.8403 (mt) cc_final: 0.8112 (tt) REVERT: L 82 ASP cc_start: 0.7209 (m-30) cc_final: 0.5796 (m-30) REVERT: H 13 GLN cc_start: 0.8869 (mm110) cc_final: 0.8574 (mm-40) REVERT: H 34 MET cc_start: 0.9032 (mmp) cc_final: 0.8770 (mmm) REVERT: H 100 ASP cc_start: 0.8793 (t0) cc_final: 0.8571 (t0) outliers start: 1 outliers final: 1 residues processed: 204 average time/residue: 0.2508 time to fit residues: 80.1794 Evaluate side-chains 161 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 8 optimal weight: 0.0170 overall best weight: 2.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN E 85 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.064791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.048296 restraints weight = 71980.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.050066 restraints weight = 42330.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.051321 restraints weight = 29805.221| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 16905 Z= 0.280 Angle : 0.677 11.347 22962 Z= 0.341 Chirality : 0.048 0.400 2879 Planarity : 0.004 0.053 2788 Dihedral : 7.451 70.778 4217 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.20), residues: 1894 helix: 0.27 (0.28), residues: 384 sheet: -0.03 (0.22), residues: 526 loop : -0.74 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 69 HIS 0.010 0.001 HIS E 85 PHE 0.016 0.002 PHE L 98 TYR 0.019 0.002 TYR L 32 ARG 0.010 0.001 ARG C 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2939.05 seconds wall clock time: 54 minutes 9.72 seconds (3249.72 seconds total)