Starting phenix.real_space_refine on Wed Apr 10 18:33:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dfg_7875/04_2024/6dfg_7875.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dfg_7875/04_2024/6dfg_7875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dfg_7875/04_2024/6dfg_7875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dfg_7875/04_2024/6dfg_7875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dfg_7875/04_2024/6dfg_7875.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dfg_7875/04_2024/6dfg_7875.pdb" } resolution = 4.42 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= 0.000 sd= 0.006 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 123 5.16 5 C 12570 2.51 5 N 3303 2.21 5 O 4194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 20190 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3427 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 5 Chain: "B" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 1, 'TRANS': 113} Chain breaks: 1 Chain: "H" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1007 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "C" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3427 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 5 Chain: "E" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 1, 'TRANS': 113} Chain breaks: 1 Chain: "G" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1007 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "J" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "D" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3427 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 5 Chain: "F" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 1, 'TRANS': 113} Chain breaks: 1 Chain: "I" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1007 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "K" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "M" 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: "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: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 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: "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: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 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: "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: 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: "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: 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: 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: "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: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 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: "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: "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: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" 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: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" 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: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.61, per 1000 atoms: 0.53 Number of scatterers: 20190 At special positions: 0 Unit cell: (158.62, 166.86, 142.14, 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 123 16.00 O 4194 8.00 N 3303 7.00 C 12570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=1.95 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.02 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=1.99 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.02 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.02 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.14 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN S 8 " - " MAN S 9 " " MAN U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " " MAN Z 4 " - " MAN Z 5 " " MAN c 4 " - " MAN c 5 " " MAN c 5 " - " MAN c 6 " " MAN c 8 " - " MAN c 9 " " MAN e 4 " - " MAN e 5 " " MAN e 5 " - " MAN e 6 " " MAN j 4 " - " MAN j 5 " " MAN m 4 " - " MAN m 5 " " MAN m 5 " - " MAN m 6 " " MAN m 8 " - " MAN m 9 " " MAN o 4 " - " MAN o 5 " " MAN o 5 " - " MAN o 6 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA P 3 " - " MAN P 4 " " BMA S 3 " - " MAN S 4 " " MAN S 7 " - " MAN S 10 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA Z 3 " - " MAN Z 4 " " BMA c 3 " - " MAN c 4 " " MAN c 7 " - " MAN c 10 " " BMA e 3 " - " MAN e 4 " " BMA g 3 " - " MAN g 4 " " BMA j 3 " - " MAN j 4 " " BMA m 3 " - " MAN m 4 " " MAN m 7 " - " MAN m 10 " " BMA o 3 " - " MAN o 4 " ALPHA1-6 " BMA P 3 " - " MAN P 6 " " BMA S 3 " - " MAN S 7 " " MAN S 7 " - " MAN S 8 " " BMA Z 3 " - " MAN Z 6 " " BMA c 3 " - " MAN c 7 " " MAN c 7 " - " MAN c 8 " " BMA j 3 " - " MAN j 6 " " BMA m 3 " - " MAN m 7 " " MAN m 7 " - " MAN m 8 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG 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 W 2 " - " BMA W 3 " " 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 b 2 " - " BMA b 3 " " 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 e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG A 605 " - " ASN A 137 " " NAG A 608 " - " ASN A 160 " " NAG A 611 " - " ASN A 234 " " NAG A 623 " - " ASN A 301 " " NAG A 634 " - " ASN A 339 " " NAG C 605 " - " ASN C 137 " " NAG C 608 " - " ASN C 160 " " NAG C 611 " - " ASN C 234 " " NAG C 623 " - " ASN C 301 " " NAG C 634 " - " ASN C 339 " " NAG D 605 " - " ASN D 137 " " NAG D 608 " - " ASN D 160 " " NAG D 611 " - " ASN D 234 " " NAG D 623 " - " ASN D 301 " " NAG D 634 " - " ASN D 339 " " NAG G 301 " - " ASN G 26 " " NAG H 301 " - " ASN H 26 " " NAG I 301 " - " ASN I 26 " " NAG M 1 " - " ASN A 133 " " NAG N 1 " - " ASN A 156 " " NAG O 1 " - " ASN A 197 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 276 " " NAG R 1 " - " ASN A 295 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 392 " " NAG V 1 " - " ASN A 448 " " NAG W 1 " - " ASN C 133 " " NAG X 1 " - " ASN C 156 " " NAG Y 1 " - " ASN C 197 " " NAG Z 1 " - " ASN C 262 " " NAG a 1 " - " ASN C 276 " " NAG b 1 " - " ASN C 295 " " NAG c 1 " - " ASN C 332 " " NAG d 1 " - " ASN C 386 " " NAG e 1 " - " ASN C 392 " " NAG f 1 " - " ASN C 448 " " NAG g 1 " - " ASN D 133 " " NAG h 1 " - " ASN D 156 " " NAG i 1 " - " ASN D 197 " " NAG j 1 " - " ASN D 262 " " NAG k 1 " - " ASN D 276 " " NAG l 1 " - " ASN D 295 " " NAG m 1 " - " ASN D 332 " " NAG n 1 " - " ASN D 386 " " NAG o 1 " - " ASN D 392 " " NAG p 1 " - " ASN D 448 " Time building additional restraints: 10.15 Conformation dependent library (CDL) restraints added in 3.4 seconds 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4386 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 51 sheets defined 16.1% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.009A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 108 " --> pdb=" O MET A 104 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 4.090A pdb=" N LYS A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 removed outlier: 3.517A pdb=" N LEU A 390 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 391 " --> pdb=" O SER A 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 387 through 391' Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.647A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 475 through 482 removed outlier: 3.697A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 537 removed outlier: 3.701A pdb=" N LEU B 537 " --> pdb=" O SER B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 removed outlier: 4.450A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 538 through 543' Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 587 through 597 removed outlier: 3.557A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE B 595 " --> pdb=" O GLN B 591 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 597 " --> pdb=" O LEU B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 639 through 646 Processing helix chain 'B' and resid 648 through 653 removed outlier: 3.920A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 657 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 27 through 30 Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.009A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 108 " --> pdb=" O MET C 104 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.091A pdb=" N LYS C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 4.335A 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 387 through 391 removed outlier: 3.517A pdb=" N LEU C 390 " --> pdb=" O THR C 387 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C 391 " --> pdb=" O SER C 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 387 through 391' Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.648A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 429' Processing helix chain 'C' and resid 475 through 482 removed outlier: 3.697A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 537 removed outlier: 3.700A pdb=" N LEU E 537 " --> pdb=" O SER E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 543 removed outlier: 4.450A pdb=" N ARG E 542 " --> pdb=" O THR E 538 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 538 through 543' Processing helix chain 'E' and resid 580 through 585 Processing helix chain 'E' and resid 587 through 597 removed outlier: 3.558A pdb=" N LEU E 592 " --> pdb=" O ARG E 588 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE E 595 " --> pdb=" O GLN E 591 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY E 597 " --> pdb=" O LEU E 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 Processing helix chain 'E' and resid 639 through 646 Processing helix chain 'E' and resid 648 through 653 removed outlier: 3.921A pdb=" N GLN E 653 " --> pdb=" O SER E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 657 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'J' and resid 27 through 30 Processing helix chain 'D' and resid 98 through 116 removed outlier: 4.009A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE D 108 " --> pdb=" O MET D 104 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 354 removed outlier: 4.090A pdb=" N LYS D 344 " --> pdb=" O GLU D 340 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL D 345 " --> pdb=" O THR D 341 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.517A pdb=" N LEU D 390 " --> pdb=" O THR D 387 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE D 391 " --> pdb=" O SER D 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 387 through 391' Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.647A pdb=" N GLN D 428 " --> pdb=" O ASN D 425 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG D 429 " --> pdb=" O MET D 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 425 through 429' Processing helix chain 'D' and resid 475 through 482 removed outlier: 3.697A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 537 removed outlier: 3.701A pdb=" N LEU F 537 " --> pdb=" O SER F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 removed outlier: 4.449A pdb=" N ARG F 542 " --> pdb=" O THR F 538 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 538 through 543' Processing helix chain 'F' and resid 580 through 585 Processing helix chain 'F' and resid 587 through 597 removed outlier: 3.558A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE F 595 " --> pdb=" O GLN F 591 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY F 597 " --> pdb=" O LEU F 593 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 Processing helix chain 'F' and resid 639 through 646 Processing helix chain 'F' and resid 648 through 653 removed outlier: 3.920A pdb=" N GLN F 653 " --> pdb=" O SER F 649 " (cutoff:3.500A) Processing helix chain 'F' and resid 654 through 657 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'K' and resid 27 through 30 Processing sheet with id=AA1, first strand: chain 'A' and resid 498 through 499 removed outlier: 6.002A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 38 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS B 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47 removed outlier: 4.060A pdb=" N LYS A 46 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 224 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 4.371A 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 54 removed outlier: 3.726A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 93 removed outlier: 3.625A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133 removed outlier: 3.586A pdb=" N SER A 174 " --> pdb=" O CYS A 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 203 removed outlier: 5.835A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET A 434 " --> pdb=" O ILE A 424 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.584A pdb=" N ILE A 271 " --> pdb=" O GLN A 287 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.519A pdb=" N CYS A 331 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 302 through 308 removed outlier: 6.223A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.557A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.557A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.711A pdb=" N TRP H 35 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.991A pdb=" N CYS H 92 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL H 102 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG H 94 " --> pdb=" O MET H 100M" (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET H 100M" --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA H 96 " --> pdb=" O TYR H 100K" (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AB7, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.198A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.198A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER L 90 " --> pdb=" O MET L 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 498 through 499 removed outlier: 5.883A pdb=" N VAL C 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR E 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N CYS E 604 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 46 through 47 removed outlier: 4.060A pdb=" N LYS C 46 " --> pdb=" O LYS C 490 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 224 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.726A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.626A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 130 through 133 removed outlier: 3.586A pdb=" N SER C 174 " --> pdb=" O CYS C 157 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC6, first strand: chain 'C' and resid 200 through 203 removed outlier: 5.835A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET C 434 " --> pdb=" O ILE C 424 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.586A pdb=" N ILE C 271 " --> pdb=" O GLN C 287 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.518A pdb=" N CYS C 331 " --> pdb=" O LEU C 416 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN C 295 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 302 through 308 removed outlier: 6.222A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.556A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.556A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.711A pdb=" N TRP G 35 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP G 50 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.991A pdb=" N CYS G 92 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL G 102 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG G 94 " --> pdb=" O MET G 100M" (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET G 100M" --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA G 96 " --> pdb=" O TYR G 100K" (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AD6, first strand: chain 'J' and resid 9 through 13 removed outlier: 6.199A pdb=" N VAL J 11 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP J 85 " --> pdb=" O GLN J 38 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR J 87 " --> pdb=" O TYR J 36 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TRP J 35 " --> pdb=" O ILE J 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 9 through 13 removed outlier: 6.199A pdb=" N VAL J 11 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER J 90 " --> pdb=" O MET J 97 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 498 through 499 removed outlier: 6.159A pdb=" N VAL D 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR F 606 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 38 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS F 604 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 46 through 47 removed outlier: 4.060A pdb=" N LYS D 46 " --> pdb=" O LYS D 490 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA D 224 " --> pdb=" O VAL D 489 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.726A pdb=" N PHE D 53 " --> pdb=" O CYS D 218 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.625A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY D 237 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 130 through 133 removed outlier: 3.586A pdb=" N SER D 174 " --> pdb=" O CYS D 157 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AE5, first strand: chain 'D' and resid 200 through 203 removed outlier: 5.835A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET D 434 " --> pdb=" O ILE D 424 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 271 through 273 removed outlier: 3.585A pdb=" N ILE D 271 " --> pdb=" O GLN D 287 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 374 through 378 removed outlier: 3.518A pdb=" N CYS D 331 " --> pdb=" O LEU D 416 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN D 295 " --> pdb=" O ASN D 332 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 302 through 308 removed outlier: 6.222A pdb=" N LYS D 305 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N THR D 320 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE D 307 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N TYR D 318 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.555A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.555A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.710A pdb=" N TRP I 35 " --> pdb=" O ASP I 50 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP I 50 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.991A pdb=" N CYS I 92 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL I 102 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG I 94 " --> pdb=" O MET I 100M" (cutoff:3.500A) removed outlier: 4.438A pdb=" N MET I 100M" --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA I 96 " --> pdb=" O TYR I 100K" (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AF5, first strand: chain 'K' and resid 9 through 13 removed outlier: 6.198A pdb=" N VAL K 11 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR K 87 " --> pdb=" O TYR K 36 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TRP K 35 " --> pdb=" O ILE K 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 9 through 13 removed outlier: 6.198A pdb=" N VAL K 11 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER K 90 " --> pdb=" O MET K 97 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1461 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: 7.32 Time building geometry restraints manager: 10.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6156 1.34 - 1.46: 5223 1.46 - 1.58: 9033 1.58 - 1.70: 3 1.70 - 1.82: 168 Bond restraints: 20583 Sorted by residual: bond pdb=" C1 MAN S 10 " pdb=" O5 MAN S 10 " ideal model delta sigma weight residual 1.399 1.487 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C1 MAN m 10 " pdb=" O5 MAN m 10 " ideal model delta sigma weight residual 1.399 1.486 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C1 MAN c 10 " pdb=" O5 MAN c 10 " ideal model delta sigma weight residual 1.399 1.486 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C1 MAN c 10 " pdb=" C2 MAN c 10 " ideal model delta sigma weight residual 1.526 1.606 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C1 MAN m 10 " pdb=" C2 MAN m 10 " ideal model delta sigma weight residual 1.526 1.605 -0.079 2.00e-02 2.50e+03 1.58e+01 ... (remaining 20578 not shown) Histogram of bond angle deviations from ideal: 99.23 - 106.24: 632 106.24 - 113.26: 12171 113.26 - 120.27: 6802 120.27 - 127.29: 8064 127.29 - 134.30: 294 Bond angle restraints: 27963 Sorted by residual: angle pdb=" C ASN D 136 " pdb=" N ASN D 137 " pdb=" CA ASN D 137 " ideal model delta sigma weight residual 121.54 132.82 -11.28 1.91e+00 2.74e-01 3.49e+01 angle pdb=" C ASN A 136 " pdb=" N ASN A 137 " pdb=" CA ASN A 137 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C ASN C 136 " pdb=" N ASN C 137 " pdb=" CA ASN C 137 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C ASN C 137 " pdb=" N ILE C 138 " pdb=" CA ILE C 138 " ideal model delta sigma weight residual 121.97 131.25 -9.28 1.80e+00 3.09e-01 2.66e+01 angle pdb=" C ASN D 137 " pdb=" N ILE D 138 " pdb=" CA ILE D 138 " ideal model delta sigma weight residual 121.97 131.23 -9.26 1.80e+00 3.09e-01 2.64e+01 ... (remaining 27958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.50: 13315 22.50 - 45.00: 465 45.00 - 67.51: 133 67.51 - 90.01: 94 90.01 - 112.51: 60 Dihedral angle restraints: 14067 sinusoidal: 7278 harmonic: 6789 Sorted by residual: dihedral pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " pdb=" CB CYS D 196 " ideal model delta sinusoidal sigma weight residual 93.00 174.86 -81.86 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 174.86 -81.86 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 174.84 -81.84 1 1.00e+01 1.00e-02 8.24e+01 ... (remaining 14064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 3140 0.099 - 0.198: 367 0.198 - 0.297: 30 0.297 - 0.396: 21 0.396 - 0.495: 3 Chirality restraints: 3561 Sorted by residual: chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN C 197 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN A 197 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.88e+00 chirality pdb=" C1 NAG i 1 " pdb=" ND2 ASN D 197 " pdb=" C2 NAG i 1 " pdb=" O5 NAG i 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.84e+00 ... (remaining 3558 not shown) Planarity restraints: 3393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN H 26 " -0.035 2.00e-02 2.50e+03 3.62e-02 1.64e+01 pdb=" CG ASN H 26 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN H 26 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN H 26 " 0.053 2.00e-02 2.50e+03 pdb=" C1 NAG H 301 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 197 " 0.040 2.00e-02 2.50e+03 3.62e-02 1.64e+01 pdb=" CG ASN C 197 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN C 197 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 197 " -0.039 2.00e-02 2.50e+03 pdb=" C1 NAG Y 1 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 197 " 0.040 2.00e-02 2.50e+03 3.55e-02 1.58e+01 pdb=" CG ASN A 197 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN A 197 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 197 " -0.038 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.040 2.00e-02 2.50e+03 ... (remaining 3390 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3928 2.77 - 3.30: 18011 3.30 - 3.84: 32493 3.84 - 4.37: 36517 4.37 - 4.90: 60722 Nonbonded interactions: 151671 Sorted by model distance: nonbonded pdb=" OD2 ASP H 50 " pdb=" O3 MAN U 6 " model vdw 2.240 2.440 nonbonded pdb=" NE2 HIS H 33 " pdb=" O2 MAN S 9 " model vdw 2.259 2.520 nonbonded pdb=" NH1 ARG H 29 " pdb=" O5 MAN S 7 " model vdw 2.263 2.520 nonbonded pdb=" O LEU F 646 " pdb=" ND2 ASN F 651 " model vdw 2.266 2.520 nonbonded pdb=" O LEU E 646 " pdb=" ND2 ASN E 651 " model vdw 2.267 2.520 ... (remaining 151666 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'W' selection = chain 'g' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'n' selection = chain 'p' } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'Z' selection = chain 'e' selection = chain 'j' selection = chain 'o' } ncs_group { reference = chain 'R' selection = chain 'b' selection = chain 'l' } ncs_group { reference = chain 'S' selection = chain 'c' selection = chain 'm' } 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: 1.540 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: 6.400 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 55.410 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 20583 Z= 0.479 Angle : 1.184 11.276 27963 Z= 0.568 Chirality : 0.069 0.495 3561 Planarity : 0.007 0.060 3345 Dihedral : 16.006 112.510 9564 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 0.29 % Allowed : 3.90 % Favored : 95.81 % 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: -4.24 (0.15), residues: 2295 helix: -4.06 (0.14), residues: 324 sheet: -1.95 (0.18), residues: 693 loop : -3.05 (0.15), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP B 614 HIS 0.007 0.002 HIS B 585 PHE 0.025 0.003 PHE I 78 TYR 0.031 0.004 TYR G 53 ARG 0.008 0.001 ARG H 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 286 time to evaluate : 2.239 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: A 95 MET cc_start: 0.8618 (ptm) cc_final: 0.7899 (ppp) REVERT: A 99 ASN cc_start: 0.8935 (m-40) cc_final: 0.8238 (t0) REVERT: A 195 ASN cc_start: 0.9061 (p0) cc_final: 0.8770 (p0) REVERT: B 606 THR cc_start: 0.8695 (p) cc_final: 0.8330 (t) REVERT: B 608 VAL cc_start: 0.9286 (p) cc_final: 0.9048 (p) REVERT: B 630 GLN cc_start: 0.9401 (mt0) cc_final: 0.9132 (mp10) REVERT: H 89 MET cc_start: 0.8723 (tpp) cc_final: 0.8368 (tpp) REVERT: L 97 MET cc_start: 0.8630 (pmm) cc_final: 0.8425 (pmm) REVERT: C 95 MET cc_start: 0.8539 (ptm) cc_final: 0.8027 (ppp) REVERT: C 195 ASN cc_start: 0.9091 (p0) cc_final: 0.8735 (p0) REVERT: E 574 LYS cc_start: 0.6968 (pttt) cc_final: 0.6638 (pttp) REVERT: E 606 THR cc_start: 0.8556 (p) cc_final: 0.8314 (t) REVERT: E 608 VAL cc_start: 0.9269 (p) cc_final: 0.9004 (p) REVERT: E 630 GLN cc_start: 0.9422 (mt0) cc_final: 0.9123 (mp10) REVERT: G 5 ARG cc_start: 0.8054 (ttt180) cc_final: 0.7818 (mtm-85) REVERT: G 32 ASP cc_start: 0.8282 (m-30) cc_final: 0.8065 (m-30) REVERT: G 89 MET cc_start: 0.8794 (tpp) cc_final: 0.8581 (tpp) REVERT: D 95 MET cc_start: 0.8695 (ptm) cc_final: 0.8137 (ppp) REVERT: D 99 ASN cc_start: 0.8838 (m-40) cc_final: 0.8248 (t0) REVERT: D 195 ASN cc_start: 0.9105 (p0) cc_final: 0.8515 (p0) REVERT: D 323 ILE cc_start: 0.9509 (OUTLIER) cc_final: 0.9243 (mp) REVERT: F 530 MET cc_start: 0.7685 (tpt) cc_final: 0.7281 (tpt) REVERT: F 542 ARG cc_start: 0.8449 (ptm-80) cc_final: 0.7769 (ttp80) REVERT: F 606 THR cc_start: 0.8600 (p) cc_final: 0.8288 (t) REVERT: F 608 VAL cc_start: 0.9153 (p) cc_final: 0.8881 (p) REVERT: F 648 GLU cc_start: 0.8644 (tt0) cc_final: 0.8364 (pt0) outliers start: 6 outliers final: 0 residues processed: 292 average time/residue: 0.4065 time to fit residues: 170.3334 Evaluate side-chains 144 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.9990 chunk 172 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 178 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 207 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN H 73 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 GLN G 100JHIS ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN ** F 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 GLN I 100JHIS ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 20583 Z= 0.282 Angle : 0.838 10.498 27963 Z= 0.406 Chirality : 0.051 0.298 3561 Planarity : 0.005 0.062 3345 Dihedral : 14.496 73.206 5238 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.59 % Favored : 89.28 % Rotamer: Outliers : 0.19 % Allowed : 2.65 % Favored : 97.16 % 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: -3.52 (0.15), residues: 2295 helix: -2.99 (0.21), residues: 336 sheet: -1.52 (0.20), residues: 606 loop : -2.64 (0.15), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 596 HIS 0.008 0.002 HIS A 352 PHE 0.012 0.002 PHE G 78 TYR 0.023 0.002 TYR H 59 ARG 0.008 0.001 ARG H 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 204 time to evaluate : 2.317 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: A 95 MET cc_start: 0.8683 (ptm) cc_final: 0.8289 (ppp) REVERT: A 99 ASN cc_start: 0.8827 (m-40) cc_final: 0.8295 (t0) REVERT: A 195 ASN cc_start: 0.9075 (p0) cc_final: 0.8792 (p0) REVERT: B 607 ASN cc_start: 0.8864 (p0) cc_final: 0.8387 (m-40) REVERT: B 651 ASN cc_start: 0.7346 (m-40) cc_final: 0.6058 (m-40) REVERT: H 86 ASP cc_start: 0.8011 (m-30) cc_final: 0.7593 (m-30) REVERT: H 89 MET cc_start: 0.8664 (tpp) cc_final: 0.8451 (tpp) REVERT: L 4 LEU cc_start: 0.8288 (mt) cc_final: 0.7910 (mt) REVERT: C 195 ASN cc_start: 0.9090 (p0) cc_final: 0.8853 (p0) REVERT: E 574 LYS cc_start: 0.7065 (pttt) cc_final: 0.6786 (pttp) REVERT: E 607 ASN cc_start: 0.8792 (p0) cc_final: 0.8266 (m-40) REVERT: E 651 ASN cc_start: 0.7205 (m-40) cc_final: 0.6071 (m-40) REVERT: G 82 MET cc_start: 0.7133 (mmp) cc_final: 0.6896 (mmt) REVERT: G 86 ASP cc_start: 0.8184 (m-30) cc_final: 0.7835 (m-30) REVERT: J 4 LEU cc_start: 0.8822 (mt) cc_final: 0.8481 (mt) REVERT: J 17 GLN cc_start: 0.8756 (mp10) cc_final: 0.8542 (mp10) REVERT: D 95 MET cc_start: 0.8747 (ptm) cc_final: 0.8467 (ppp) REVERT: D 99 ASN cc_start: 0.8828 (m-40) cc_final: 0.8311 (t0) REVERT: D 195 ASN cc_start: 0.9086 (p0) cc_final: 0.8652 (p0) REVERT: F 542 ARG cc_start: 0.8532 (ptm-80) cc_final: 0.7933 (ttp80) REVERT: F 607 ASN cc_start: 0.8763 (p0) cc_final: 0.8421 (m-40) REVERT: F 651 ASN cc_start: 0.7865 (m-40) cc_final: 0.6861 (m-40) REVERT: F 652 GLN cc_start: 0.8064 (mp10) cc_final: 0.7741 (mp10) REVERT: F 660 LEU cc_start: 0.8671 (mm) cc_final: 0.8429 (pp) REVERT: I 63 LEU cc_start: 0.9085 (mt) cc_final: 0.8872 (mt) outliers start: 4 outliers final: 3 residues processed: 208 average time/residue: 0.3607 time to fit residues: 111.7484 Evaluate side-chains 134 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 131 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 172 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 224 optimal weight: 20.0000 chunk 184 optimal weight: 0.2980 chunk 205 optimal weight: 5.9990 chunk 70 optimal weight: 0.0570 chunk 166 optimal weight: 8.9990 overall best weight: 4.2704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN E 591 GLN E 652 GLN ** E 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20583 Z= 0.285 Angle : 0.792 9.280 27963 Z= 0.377 Chirality : 0.049 0.290 3561 Planarity : 0.005 0.047 3345 Dihedral : 11.856 66.580 5238 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.63 % Favored : 89.24 % Rotamer: Outliers : 0.14 % Allowed : 3.47 % Favored : 96.39 % 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: -3.20 (0.16), residues: 2295 helix: -2.08 (0.24), residues: 375 sheet: -1.37 (0.19), residues: 645 loop : -2.61 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 628 HIS 0.006 0.002 HIS A 352 PHE 0.016 0.002 PHE G 78 TYR 0.016 0.002 TYR E 643 ARG 0.010 0.001 ARG I 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 175 time to evaluate : 2.283 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: A 95 MET cc_start: 0.8671 (ptm) cc_final: 0.8252 (ppp) REVERT: A 99 ASN cc_start: 0.8851 (m-40) cc_final: 0.8287 (t0) REVERT: A 195 ASN cc_start: 0.8938 (p0) cc_final: 0.8639 (p0) REVERT: B 607 ASN cc_start: 0.8809 (p0) cc_final: 0.8225 (m110) REVERT: B 626 MET cc_start: 0.8911 (mpp) cc_final: 0.8496 (mmm) REVERT: B 630 GLN cc_start: 0.8737 (pp30) cc_final: 0.8114 (pp30) REVERT: B 651 ASN cc_start: 0.7461 (m-40) cc_final: 0.7196 (m-40) REVERT: H 18 LEU cc_start: 0.9260 (tt) cc_final: 0.8970 (tt) REVERT: H 82 MET cc_start: 0.9043 (tmm) cc_final: 0.8727 (tmm) REVERT: H 86 ASP cc_start: 0.8161 (m-30) cc_final: 0.7918 (m-30) REVERT: H 89 MET cc_start: 0.8677 (tpp) cc_final: 0.8373 (tpp) REVERT: H 100 LEU cc_start: 0.9097 (tp) cc_final: 0.8571 (tp) REVERT: H 100 GLU cc_start: 0.8838 (mm-30) cc_final: 0.7952 (mp0) REVERT: L 4 LEU cc_start: 0.8453 (mt) cc_final: 0.8244 (mp) REVERT: C 95 MET cc_start: 0.8544 (ppp) cc_final: 0.8174 (ppp) REVERT: C 195 ASN cc_start: 0.9042 (p0) cc_final: 0.8815 (p0) REVERT: E 574 LYS cc_start: 0.7023 (pttt) cc_final: 0.6740 (pttp) REVERT: E 607 ASN cc_start: 0.8763 (p0) cc_final: 0.8187 (m110) REVERT: E 630 GLN cc_start: 0.9435 (mt0) cc_final: 0.9077 (tm-30) REVERT: E 651 ASN cc_start: 0.7309 (m-40) cc_final: 0.6310 (m-40) REVERT: G 82 MET cc_start: 0.9078 (tmm) cc_final: 0.8807 (tmm) REVERT: G 82 MET cc_start: 0.7222 (mmp) cc_final: 0.6780 (mmt) REVERT: D 95 MET cc_start: 0.8759 (ptm) cc_final: 0.8426 (ppp) REVERT: D 99 ASN cc_start: 0.8790 (m-40) cc_final: 0.8277 (t0) REVERT: D 195 ASN cc_start: 0.8930 (p0) cc_final: 0.8467 (p0) REVERT: F 591 GLN cc_start: 0.8374 (pt0) cc_final: 0.8011 (tt0) REVERT: F 607 ASN cc_start: 0.8721 (p0) cc_final: 0.8268 (m110) REVERT: F 651 ASN cc_start: 0.7710 (m-40) cc_final: 0.7411 (m-40) REVERT: F 660 LEU cc_start: 0.8718 (mm) cc_final: 0.8483 (pp) REVERT: I 63 LEU cc_start: 0.9139 (mt) cc_final: 0.8899 (mt) REVERT: I 64 ARG cc_start: 0.9150 (mtp-110) cc_final: 0.8891 (mtp85) outliers start: 3 outliers final: 0 residues processed: 178 average time/residue: 0.3614 time to fit residues: 96.8112 Evaluate side-chains 126 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 107 optimal weight: 0.0170 chunk 22 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 139 optimal weight: 30.0000 chunk 208 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 197 optimal weight: 0.0370 chunk 59 optimal weight: 9.9990 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN ** E 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN ** F 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20583 Z= 0.167 Angle : 0.711 9.743 27963 Z= 0.340 Chirality : 0.048 0.338 3561 Planarity : 0.004 0.043 3345 Dihedral : 10.328 64.494 5238 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % 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: -2.61 (0.17), residues: 2295 helix: -1.58 (0.27), residues: 327 sheet: -0.97 (0.20), residues: 660 loop : -2.25 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 596 HIS 0.003 0.001 HIS H 33 PHE 0.016 0.001 PHE H 78 TYR 0.024 0.001 TYR I 90 ARG 0.007 0.000 ARG G 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 2.384 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: A 99 ASN cc_start: 0.8845 (m-40) cc_final: 0.8472 (t0) REVERT: A 195 ASN cc_start: 0.8941 (p0) cc_final: 0.8646 (p0) REVERT: B 607 ASN cc_start: 0.8801 (p0) cc_final: 0.8307 (m-40) REVERT: B 651 ASN cc_start: 0.7395 (m-40) cc_final: 0.6391 (m-40) REVERT: H 63 LEU cc_start: 0.8699 (mt) cc_final: 0.8494 (mt) REVERT: H 86 ASP cc_start: 0.8146 (m-30) cc_final: 0.7887 (m-30) REVERT: H 100 MET cc_start: 0.6845 (mmm) cc_final: 0.6535 (mmm) REVERT: L 4 LEU cc_start: 0.8390 (mt) cc_final: 0.7883 (mt) REVERT: C 95 MET cc_start: 0.8322 (ppp) cc_final: 0.7910 (ppp) REVERT: C 195 ASN cc_start: 0.8994 (p0) cc_final: 0.8714 (p0) REVERT: E 607 ASN cc_start: 0.8722 (p0) cc_final: 0.8236 (m-40) REVERT: E 630 GLN cc_start: 0.9337 (mt0) cc_final: 0.9055 (mt0) REVERT: E 651 ASN cc_start: 0.7120 (m-40) cc_final: 0.6732 (m-40) REVERT: G 63 LEU cc_start: 0.9064 (mt) cc_final: 0.8862 (mt) REVERT: G 86 ASP cc_start: 0.8079 (m-30) cc_final: 0.7807 (m-30) REVERT: G 100 GLU cc_start: 0.8756 (mm-30) cc_final: 0.7755 (mp0) REVERT: J 4 LEU cc_start: 0.8803 (mt) cc_final: 0.8561 (mt) REVERT: D 99 ASN cc_start: 0.8758 (m-40) cc_final: 0.8270 (t0) REVERT: D 104 MET cc_start: 0.8487 (tpt) cc_final: 0.8237 (tpt) REVERT: D 195 ASN cc_start: 0.8997 (p0) cc_final: 0.8661 (p0) REVERT: D 217 TYR cc_start: 0.6473 (m-10) cc_final: 0.4891 (m-80) REVERT: F 607 ASN cc_start: 0.8649 (p0) cc_final: 0.8322 (m-40) REVERT: F 626 MET cc_start: 0.7785 (tmm) cc_final: 0.7197 (tmm) REVERT: F 660 LEU cc_start: 0.8676 (mm) cc_final: 0.8461 (pp) REVERT: I 63 LEU cc_start: 0.9161 (mt) cc_final: 0.8903 (mt) REVERT: I 64 ARG cc_start: 0.9118 (mtp-110) cc_final: 0.8764 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.3334 time to fit residues: 90.1883 Evaluate side-chains 129 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 3 optimal weight: 0.9990 chunk 164 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 188 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 197 optimal weight: 10.0000 chunk 55 optimal weight: 0.4980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN ** E 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 20583 Z= 0.162 Angle : 0.688 9.586 27963 Z= 0.328 Chirality : 0.048 0.358 3561 Planarity : 0.004 0.044 3345 Dihedral : 9.377 61.959 5238 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: -2.39 (0.17), residues: 2295 helix: -1.13 (0.30), residues: 291 sheet: -0.76 (0.20), residues: 675 loop : -2.22 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 112 HIS 0.004 0.001 HIS E 585 PHE 0.013 0.001 PHE C 382 TYR 0.019 0.001 TYR H 90 ARG 0.005 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.297 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: A 95 MET cc_start: 0.8331 (ppp) cc_final: 0.7736 (ppp) REVERT: A 99 ASN cc_start: 0.8925 (m-40) cc_final: 0.8432 (t0) REVERT: A 195 ASN cc_start: 0.8959 (p0) cc_final: 0.8695 (p0) REVERT: B 607 ASN cc_start: 0.8749 (p0) cc_final: 0.8290 (m-40) REVERT: B 651 ASN cc_start: 0.7551 (m-40) cc_final: 0.6498 (m-40) REVERT: H 63 LEU cc_start: 0.8708 (mt) cc_final: 0.8500 (mt) REVERT: H 86 ASP cc_start: 0.8190 (m-30) cc_final: 0.7888 (m-30) REVERT: L 4 LEU cc_start: 0.8477 (mt) cc_final: 0.8030 (mt) REVERT: C 95 MET cc_start: 0.8206 (ppp) cc_final: 0.7728 (ppp) REVERT: C 195 ASN cc_start: 0.9042 (p0) cc_final: 0.8769 (p0) REVERT: E 591 GLN cc_start: 0.8812 (tp-100) cc_final: 0.8565 (tt0) REVERT: E 607 ASN cc_start: 0.8763 (p0) cc_final: 0.8268 (m110) REVERT: E 630 GLN cc_start: 0.9388 (mt0) cc_final: 0.9064 (tm-30) REVERT: E 651 ASN cc_start: 0.7120 (m-40) cc_final: 0.6064 (m-40) REVERT: G 63 LEU cc_start: 0.9049 (mt) cc_final: 0.8848 (mt) REVERT: G 86 ASP cc_start: 0.8126 (m-30) cc_final: 0.7826 (m-30) REVERT: G 100 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8257 (mp0) REVERT: G 103 TRP cc_start: 0.8652 (m100) cc_final: 0.8431 (m100) REVERT: J 4 LEU cc_start: 0.8819 (mt) cc_final: 0.8580 (mt) REVERT: J 17 GLN cc_start: 0.8766 (mp10) cc_final: 0.8486 (mp10) REVERT: D 95 MET cc_start: 0.8470 (ppp) cc_final: 0.7892 (ppp) REVERT: D 99 ASN cc_start: 0.8750 (m-40) cc_final: 0.8467 (t0) REVERT: D 104 MET cc_start: 0.8555 (tpt) cc_final: 0.8291 (tpt) REVERT: D 195 ASN cc_start: 0.9026 (p0) cc_final: 0.8671 (p0) REVERT: D 217 TYR cc_start: 0.6543 (m-10) cc_final: 0.4924 (m-10) REVERT: F 590 GLN cc_start: 0.8362 (tm-30) cc_final: 0.8014 (tm-30) REVERT: F 607 ASN cc_start: 0.8623 (p0) cc_final: 0.8311 (m-40) REVERT: F 657 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8302 (mm-30) REVERT: F 660 LEU cc_start: 0.8663 (mm) cc_final: 0.8436 (pp) REVERT: I 63 LEU cc_start: 0.9134 (mt) cc_final: 0.8874 (mt) REVERT: I 64 ARG cc_start: 0.9122 (mtp-110) cc_final: 0.8759 (mmm-85) REVERT: I 89 MET cc_start: 0.8587 (tpt) cc_final: 0.8004 (tpp) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.3252 time to fit residues: 89.6618 Evaluate side-chains 130 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 129 optimal weight: 0.0570 chunk 54 optimal weight: 0.9980 chunk 220 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 115 optimal weight: 30.0000 overall best weight: 3.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20583 Z= 0.219 Angle : 0.706 9.425 27963 Z= 0.336 Chirality : 0.047 0.373 3561 Planarity : 0.004 0.042 3345 Dihedral : 8.951 59.704 5238 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 0.10 % Allowed : 1.88 % Favored : 98.03 % 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: -2.30 (0.17), residues: 2295 helix: -0.95 (0.30), residues: 285 sheet: -0.74 (0.19), residues: 711 loop : -2.19 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 596 HIS 0.004 0.001 HIS D 352 PHE 0.015 0.001 PHE D 159 TYR 0.020 0.001 TYR H 90 ARG 0.006 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 2.426 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: A 95 MET cc_start: 0.8375 (ppp) cc_final: 0.8022 (ppp) REVERT: A 99 ASN cc_start: 0.8960 (m-40) cc_final: 0.8516 (t0) REVERT: A 195 ASN cc_start: 0.8954 (p0) cc_final: 0.8679 (p0) REVERT: B 607 ASN cc_start: 0.8808 (p0) cc_final: 0.8227 (m-40) REVERT: B 651 ASN cc_start: 0.7652 (m-40) cc_final: 0.7439 (m-40) REVERT: H 63 LEU cc_start: 0.8652 (mt) cc_final: 0.8438 (mt) REVERT: H 86 ASP cc_start: 0.8160 (m-30) cc_final: 0.7900 (m-30) REVERT: H 89 MET cc_start: 0.8555 (tpt) cc_final: 0.7788 (tpp) REVERT: L 4 LEU cc_start: 0.8499 (mt) cc_final: 0.8100 (mt) REVERT: C 95 MET cc_start: 0.8304 (ppp) cc_final: 0.7852 (ppp) REVERT: C 195 ASN cc_start: 0.9078 (p0) cc_final: 0.8832 (p0) REVERT: E 591 GLN cc_start: 0.8909 (tp-100) cc_final: 0.8594 (tt0) REVERT: E 607 ASN cc_start: 0.8891 (p0) cc_final: 0.8314 (m-40) REVERT: E 651 ASN cc_start: 0.7062 (m-40) cc_final: 0.6046 (m-40) REVERT: G 63 LEU cc_start: 0.9061 (mt) cc_final: 0.8846 (mt) REVERT: G 86 ASP cc_start: 0.8130 (m-30) cc_final: 0.7778 (m-30) REVERT: G 100 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8366 (mp0) REVERT: G 103 TRP cc_start: 0.8701 (m100) cc_final: 0.8474 (m100) REVERT: D 95 MET cc_start: 0.8465 (ppp) cc_final: 0.8077 (ppp) REVERT: D 99 ASN cc_start: 0.8865 (m-40) cc_final: 0.8477 (t0) REVERT: D 195 ASN cc_start: 0.8981 (p0) cc_final: 0.8644 (p0) REVERT: F 590 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8128 (tm-30) REVERT: F 607 ASN cc_start: 0.8684 (p0) cc_final: 0.8352 (m-40) REVERT: F 657 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8360 (mm-30) REVERT: I 63 LEU cc_start: 0.9160 (mt) cc_final: 0.8896 (mt) REVERT: I 64 ARG cc_start: 0.9158 (mtp-110) cc_final: 0.8756 (mmm-85) REVERT: I 89 MET cc_start: 0.8674 (tpt) cc_final: 0.8160 (tpp) REVERT: I 100 GLU cc_start: 0.8224 (mp0) cc_final: 0.7777 (mp0) outliers start: 2 outliers final: 0 residues processed: 167 average time/residue: 0.3279 time to fit residues: 85.5746 Evaluate side-chains 129 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 125 optimal weight: 20.0000 chunk 161 optimal weight: 0.0050 chunk 124 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 chunk 219 optimal weight: 10.0000 chunk 137 optimal weight: 0.6980 chunk 133 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 overall best weight: 3.1398 ------------------------------------------------------------------------------- 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** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN ** E 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** F 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20583 Z= 0.220 Angle : 0.718 9.348 27963 Z= 0.340 Chirality : 0.048 0.383 3561 Planarity : 0.004 0.045 3345 Dihedral : 8.652 57.825 5238 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.93 % Favored : 89.98 % Rotamer: Outliers : 0.05 % Allowed : 1.16 % Favored : 98.80 % 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: -2.18 (0.17), residues: 2295 helix: -0.44 (0.31), residues: 267 sheet: -0.60 (0.19), residues: 708 loop : -2.24 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 596 HIS 0.003 0.001 HIS A 352 PHE 0.015 0.002 PHE A 382 TYR 0.012 0.001 TYR H 90 ARG 0.005 0.000 ARG D 350 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 2.406 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: A 95 MET cc_start: 0.8420 (ppp) cc_final: 0.8054 (ppp) REVERT: A 99 ASN cc_start: 0.8948 (m-40) cc_final: 0.8499 (t0) REVERT: A 195 ASN cc_start: 0.8961 (p0) cc_final: 0.8671 (p0) REVERT: B 651 ASN cc_start: 0.7697 (m-40) cc_final: 0.7461 (m-40) REVERT: H 63 LEU cc_start: 0.8758 (mt) cc_final: 0.8549 (mt) REVERT: H 86 ASP cc_start: 0.8292 (m-30) cc_final: 0.8091 (m-30) REVERT: H 89 MET cc_start: 0.8609 (tpt) cc_final: 0.7933 (tpp) REVERT: H 100 LEU cc_start: 0.9184 (tp) cc_final: 0.8644 (tp) REVERT: H 100 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8055 (mp0) REVERT: L 4 LEU cc_start: 0.8783 (mt) cc_final: 0.8137 (mt) REVERT: C 95 MET cc_start: 0.8377 (ppp) cc_final: 0.7927 (ppp) REVERT: C 195 ASN cc_start: 0.9126 (p0) cc_final: 0.8827 (p0) REVERT: E 591 GLN cc_start: 0.8966 (tp-100) cc_final: 0.8659 (tt0) REVERT: G 63 LEU cc_start: 0.9073 (mt) cc_final: 0.8848 (mt) REVERT: G 86 ASP cc_start: 0.8232 (m-30) cc_final: 0.7889 (m-30) REVERT: G 100 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8306 (mp0) REVERT: D 95 MET cc_start: 0.8496 (ppp) cc_final: 0.8069 (ppp) REVERT: D 99 ASN cc_start: 0.8888 (m-40) cc_final: 0.8470 (t0) REVERT: D 195 ASN cc_start: 0.8987 (p0) cc_final: 0.8694 (p0) REVERT: F 590 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8187 (tm-30) REVERT: F 607 ASN cc_start: 0.8759 (p0) cc_final: 0.8258 (m-40) REVERT: F 630 GLN cc_start: 0.9335 (mt0) cc_final: 0.9122 (tm-30) REVERT: I 63 LEU cc_start: 0.9172 (mt) cc_final: 0.8924 (mt) REVERT: I 64 ARG cc_start: 0.9174 (mtp-110) cc_final: 0.8867 (mtp85) REVERT: I 89 MET cc_start: 0.8695 (tpt) cc_final: 0.8263 (tpp) REVERT: I 100 GLU cc_start: 0.8114 (mp0) cc_final: 0.7751 (mp0) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.3245 time to fit residues: 82.4154 Evaluate side-chains 122 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 139 optimal weight: 20.0000 chunk 149 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- 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** B 543 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 20583 Z= 0.333 Angle : 0.809 10.418 27963 Z= 0.384 Chirality : 0.049 0.384 3561 Planarity : 0.004 0.045 3345 Dihedral : 8.944 59.114 5238 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.59 % Favored : 88.28 % Rotamer: Outliers : 0.05 % Allowed : 1.69 % Favored : 98.27 % 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: -2.42 (0.17), residues: 2295 helix: -1.32 (0.28), residues: 312 sheet: -0.77 (0.19), residues: 735 loop : -2.26 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 427 HIS 0.004 0.002 HIS C 352 PHE 0.019 0.002 PHE C 382 TYR 0.022 0.002 TYR H 90 ARG 0.005 0.001 ARG D 350 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 1.847 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 95 MET cc_start: 0.8448 (ppp) cc_final: 0.8059 (ppp) REVERT: A 99 ASN cc_start: 0.9005 (m-40) cc_final: 0.8388 (t0) REVERT: A 195 ASN cc_start: 0.8963 (p0) cc_final: 0.8701 (p0) REVERT: B 607 ASN cc_start: 0.8850 (p0) cc_final: 0.8040 (m-40) REVERT: B 651 ASN cc_start: 0.7785 (m-40) cc_final: 0.7515 (m-40) REVERT: H 63 LEU cc_start: 0.8899 (mt) cc_final: 0.8682 (mt) REVERT: H 89 MET cc_start: 0.8641 (tpt) cc_final: 0.8026 (tpp) REVERT: H 100 LEU cc_start: 0.9332 (tp) cc_final: 0.9044 (tp) REVERT: H 100 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8240 (mp0) REVERT: H 100 MET cc_start: 0.7972 (mmm) cc_final: 0.7692 (mmm) REVERT: C 95 MET cc_start: 0.8453 (ppp) cc_final: 0.8206 (ppp) REVERT: C 195 ASN cc_start: 0.9146 (p0) cc_final: 0.8851 (p0) REVERT: E 607 ASN cc_start: 0.8912 (p0) cc_final: 0.8065 (m-40) REVERT: E 651 ASN cc_start: 0.7468 (m-40) cc_final: 0.7206 (m-40) REVERT: G 13 LYS cc_start: 0.7924 (mmtt) cc_final: 0.7639 (mmtm) REVERT: G 63 LEU cc_start: 0.9134 (mt) cc_final: 0.8908 (mt) REVERT: G 100 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8441 (mm-30) REVERT: D 95 MET cc_start: 0.8531 (ppp) cc_final: 0.8105 (ppp) REVERT: D 99 ASN cc_start: 0.8902 (m-40) cc_final: 0.8278 (t0) REVERT: D 195 ASN cc_start: 0.9019 (p0) cc_final: 0.8668 (p0) REVERT: F 590 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8290 (tm-30) REVERT: F 607 ASN cc_start: 0.8875 (p0) cc_final: 0.8175 (m-40) REVERT: I 43 LYS cc_start: 0.8644 (mmtt) cc_final: 0.8391 (mmtp) REVERT: I 63 LEU cc_start: 0.9180 (mt) cc_final: 0.8954 (mt) REVERT: I 89 MET cc_start: 0.8681 (tpt) cc_final: 0.8306 (tpp) REVERT: I 100 GLU cc_start: 0.8315 (mp0) cc_final: 0.8081 (mp0) outliers start: 1 outliers final: 0 residues processed: 148 average time/residue: 0.3158 time to fit residues: 74.2299 Evaluate side-chains 110 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 62 optimal weight: 30.0000 chunk 185 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 134 optimal weight: 0.0970 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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** B 543 ASN H 100JHIS ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN E 591 GLN ** E 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20583 Z= 0.173 Angle : 0.713 10.481 27963 Z= 0.338 Chirality : 0.049 0.409 3561 Planarity : 0.004 0.049 3345 Dihedral : 8.337 53.444 5238 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.06 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -2.26 (0.17), residues: 2295 helix: -0.82 (0.30), residues: 303 sheet: -0.48 (0.20), residues: 711 loop : -2.36 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP E 596 HIS 0.003 0.001 HIS C 374 PHE 0.015 0.001 PHE C 382 TYR 0.016 0.001 TYR A 217 ARG 0.006 0.000 ARG H 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8371 (ppp) cc_final: 0.7957 (ppp) REVERT: A 99 ASN cc_start: 0.8971 (m-40) cc_final: 0.8433 (t0) REVERT: A 195 ASN cc_start: 0.8918 (p0) cc_final: 0.8631 (p0) REVERT: B 607 ASN cc_start: 0.8866 (p0) cc_final: 0.8081 (m-40) REVERT: B 651 ASN cc_start: 0.7765 (m-40) cc_final: 0.7540 (m-40) REVERT: H 63 LEU cc_start: 0.8832 (mt) cc_final: 0.8597 (mt) REVERT: H 82 MET cc_start: 0.8971 (tmm) cc_final: 0.8551 (tmm) REVERT: H 89 MET cc_start: 0.8694 (tpt) cc_final: 0.8098 (tpp) REVERT: H 100 LEU cc_start: 0.9348 (tp) cc_final: 0.9007 (tp) REVERT: H 100 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8134 (mp0) REVERT: H 100 MET cc_start: 0.7884 (mmm) cc_final: 0.7633 (mmm) REVERT: L 4 LEU cc_start: 0.8868 (mt) cc_final: 0.8293 (mt) REVERT: C 95 MET cc_start: 0.8337 (ppp) cc_final: 0.8074 (ppp) REVERT: C 195 ASN cc_start: 0.9085 (p0) cc_final: 0.8747 (p0) REVERT: E 591 GLN cc_start: 0.8972 (tp-100) cc_final: 0.8605 (tt0) REVERT: E 607 ASN cc_start: 0.8903 (p0) cc_final: 0.8113 (m-40) REVERT: E 651 ASN cc_start: 0.7567 (m-40) cc_final: 0.6716 (m-40) REVERT: G 13 LYS cc_start: 0.7730 (mmtt) cc_final: 0.7244 (tppt) REVERT: G 20 LEU cc_start: 0.9213 (mt) cc_final: 0.8843 (mp) REVERT: G 63 LEU cc_start: 0.9083 (mt) cc_final: 0.8843 (mt) REVERT: G 100 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8390 (mm-30) REVERT: D 95 MET cc_start: 0.8424 (ppp) cc_final: 0.7861 (ppp) REVERT: D 99 ASN cc_start: 0.8864 (m-40) cc_final: 0.8339 (t0) REVERT: D 195 ASN cc_start: 0.8942 (p0) cc_final: 0.8705 (p0) REVERT: F 590 GLN cc_start: 0.8510 (tm-30) cc_final: 0.8178 (tm-30) REVERT: F 607 ASN cc_start: 0.8879 (p0) cc_final: 0.8173 (m-40) REVERT: I 43 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8379 (mmtp) REVERT: I 63 LEU cc_start: 0.9123 (mt) cc_final: 0.8884 (mt) REVERT: I 64 ARG cc_start: 0.9205 (mtp-110) cc_final: 0.8952 (mtp85) REVERT: I 89 MET cc_start: 0.8737 (tpt) cc_final: 0.8441 (tpp) REVERT: I 100 GLU cc_start: 0.8284 (mp0) cc_final: 0.7871 (mp0) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.3454 time to fit residues: 87.5047 Evaluate side-chains 120 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 227 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 143 optimal weight: 0.6980 overall best weight: 4.1186 ------------------------------------------------------------------------------- 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** B 543 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN E 656 ASN ** E 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20583 Z= 0.274 Angle : 0.764 10.407 27963 Z= 0.363 Chirality : 0.048 0.374 3561 Planarity : 0.004 0.044 3345 Dihedral : 8.283 58.765 5238 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.63 % Favored : 88.28 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -2.38 (0.17), residues: 2295 helix: -1.19 (0.28), residues: 324 sheet: -0.63 (0.19), residues: 735 loop : -2.35 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 623 HIS 0.004 0.001 HIS F 585 PHE 0.018 0.002 PHE C 382 TYR 0.020 0.002 TYR G 90 ARG 0.005 0.001 ARG J 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 2.527 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 95 MET cc_start: 0.8462 (ppp) cc_final: 0.8044 (ppp) REVERT: A 99 ASN cc_start: 0.8968 (m-40) cc_final: 0.8435 (t0) REVERT: A 195 ASN cc_start: 0.8966 (p0) cc_final: 0.8706 (p0) REVERT: B 607 ASN cc_start: 0.8934 (p0) cc_final: 0.8067 (m-40) REVERT: B 651 ASN cc_start: 0.7838 (m-40) cc_final: 0.7588 (m-40) REVERT: H 63 LEU cc_start: 0.8883 (mt) cc_final: 0.8657 (mt) REVERT: H 89 MET cc_start: 0.8601 (tpt) cc_final: 0.8126 (tpp) REVERT: H 100 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8293 (mp0) REVERT: C 95 MET cc_start: 0.8458 (ppp) cc_final: 0.8012 (ppp) REVERT: C 195 ASN cc_start: 0.9144 (p0) cc_final: 0.8848 (p0) REVERT: E 591 GLN cc_start: 0.8957 (tp-100) cc_final: 0.8609 (tt0) REVERT: E 607 ASN cc_start: 0.8923 (p0) cc_final: 0.8067 (m-40) REVERT: E 651 ASN cc_start: 0.7598 (m-40) cc_final: 0.6654 (m-40) REVERT: G 63 LEU cc_start: 0.9135 (mt) cc_final: 0.8906 (mt) REVERT: G 89 MET cc_start: 0.8455 (tpt) cc_final: 0.7889 (tpp) REVERT: G 100 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8518 (mm-30) REVERT: D 95 MET cc_start: 0.8515 (ppp) cc_final: 0.8055 (ppp) REVERT: D 99 ASN cc_start: 0.8883 (m-40) cc_final: 0.8364 (t0) REVERT: D 195 ASN cc_start: 0.9011 (p0) cc_final: 0.8682 (p0) REVERT: F 607 ASN cc_start: 0.8876 (p0) cc_final: 0.8152 (m-40) REVERT: I 43 LYS cc_start: 0.8709 (mmtt) cc_final: 0.8405 (mmtp) REVERT: I 63 LEU cc_start: 0.9132 (mt) cc_final: 0.8911 (mt) REVERT: I 82 MET cc_start: 0.8390 (tpt) cc_final: 0.8101 (tpt) REVERT: I 89 MET cc_start: 0.8720 (tpt) cc_final: 0.8401 (tpp) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.3228 time to fit residues: 73.7882 Evaluate side-chains 108 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 166 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 181 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 159 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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** B 543 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN ** E 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN F 543 ASN ** F 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.039152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.031926 restraints weight = 180746.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.032893 restraints weight = 105169.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.033554 restraints weight = 72389.142| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 20583 Z= 0.386 Angle : 0.864 11.844 27963 Z= 0.411 Chirality : 0.050 0.410 3561 Planarity : 0.005 0.050 3345 Dihedral : 8.891 59.966 5238 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.03 % Favored : 87.84 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.65 (0.17), residues: 2295 helix: -1.52 (0.26), residues: 336 sheet: -0.89 (0.19), residues: 765 loop : -2.46 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP E 596 HIS 0.005 0.002 HIS A 352 PHE 0.023 0.002 PHE A 382 TYR 0.033 0.002 TYR D 217 ARG 0.010 0.001 ARG F 617 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3185.65 seconds wall clock time: 60 minutes 58.96 seconds (3658.96 seconds total)