Starting phenix.real_space_refine on Sun Feb 18 00:22:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gas_29905/02_2024/8gas_29905.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gas_29905/02_2024/8gas_29905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gas_29905/02_2024/8gas_29905.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gas_29905/02_2024/8gas_29905.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gas_29905/02_2024/8gas_29905.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gas_29905/02_2024/8gas_29905.pdb" } resolution = 4.04 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= 0.013 sd= 0.074 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 129 5.16 5 C 12696 2.51 5 N 3369 2.21 5 O 4059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 466": "OE1" <-> "OE2" Residue "G PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 153": "OE1" <-> "OE2" Residue "D PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 492": "OE1" <-> "OE2" Residue "J GLU 211": "OE1" <-> "OE2" Residue "J GLU 492": "OE1" <-> "OE2" Residue "K ASP 632": "OD1" <-> "OD2" Residue "K GLU 634": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20253 Number of models: 1 Model: "" Number of chains: 39 Chain: "L" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "H" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 939 Classifications: {'peptide': 121} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 114} Chain: "G" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3472 Classifications: {'peptide': 442} Incomplete info: {'backbone_only': 1} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1059 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "A" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "C" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 939 Classifications: {'peptide': 121} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 114} Chain: "D" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3472 Classifications: {'peptide': 442} Incomplete info: {'backbone_only': 1} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1059 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 105} Chain: "I" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 939 Classifications: {'peptide': 121} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 114} Chain: "J" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3472 Classifications: {'peptide': 442} Incomplete info: {'backbone_only': 1} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1059 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "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: 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: "T" 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" 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: "a" 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 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: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} 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: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} 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: "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 Time building chain proxies: 10.64, per 1000 atoms: 0.53 Number of scatterers: 20253 At special positions: 0 Unit cell: (142.749, 150.262, 122.356, 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 129 16.00 O 4059 8.00 N 3369 7.00 C 12696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " 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=2.03 Simple disulfide: pdb=" SG CYS D 201 " - pdb=" SG CYS D 433 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 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 E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.03 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.03 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.03 Simple disulfide: pdb=" SG CYS J 201 " - pdb=" SG CYS J 433 " distance=2.04 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.03 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.03 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS K 605 " distance=2.03 Simple disulfide: pdb=" SG CYS K 598 " - pdb=" SG CYS K 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA Z 3 " - " MAN Z 4 " " BMA g 3 " - " MAN g 4 " 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 Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " NAG-ASN " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG D 601 " - " ASN D 133 " " NAG D 602 " - " ASN D 156 " " NAG D 603 " - " ASN D 160 " " NAG D 604 " - " ASN D 197 " " NAG D 605 " - " ASN D 276 " " NAG D 606 " - " ASN D 301 " " NAG D 607 " - " ASN D 355 " " NAG D 608 " - " ASN D 339 " " NAG D 609 " - " ASN D 392 " " NAG D 610 " - " ASN D 234 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 156 " " NAG G 603 " - " ASN G 160 " " NAG G 604 " - " ASN G 197 " " NAG G 605 " - " ASN G 276 " " NAG G 606 " - " ASN G 301 " " NAG G 607 " - " ASN G 355 " " NAG G 608 " - " ASN G 339 " " NAG G 609 " - " ASN G 392 " " NAG G 610 " - " ASN G 234 " " NAG J 601 " - " ASN J 133 " " NAG J 602 " - " ASN J 156 " " NAG J 603 " - " ASN J 160 " " NAG J 604 " - " ASN J 197 " " NAG J 605 " - " ASN J 276 " " NAG J 606 " - " ASN J 301 " " NAG J 607 " - " ASN J 355 " " NAG J 608 " - " ASN J 339 " " NAG J 609 " - " ASN J 392 " " NAG J 610 " - " ASN J 234 " " NAG K 701 " - " ASN K 611 " " NAG K 702 " - " ASN K 637 " " NAG M 1 " - " ASN G 88 " " NAG N 1 " - " ASN G 295 " " NAG O 1 " - " ASN G 332 " " NAG P 1 " - " ASN G 363 " " NAG Q 1 " - " ASN G 386 " " NAG R 1 " - " ASN G 448 " " NAG S 1 " - " ASN G 262 " " NAG T 1 " - " ASN D 88 " " NAG U 1 " - " ASN D 295 " " NAG V 1 " - " ASN D 332 " " NAG W 1 " - " ASN D 363 " " NAG X 1 " - " ASN D 386 " " NAG Y 1 " - " ASN D 448 " " NAG Z 1 " - " ASN D 262 " " NAG a 1 " - " ASN J 88 " " NAG b 1 " - " ASN J 295 " " NAG c 1 " - " ASN J 332 " " NAG d 1 " - " ASN J 363 " " NAG e 1 " - " ASN J 386 " " NAG f 1 " - " ASN J 448 " " NAG g 1 " - " ASN J 262 " Time building additional restraints: 9.07 Conformation dependent library (CDL) restraints added in 3.5 seconds 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4470 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 39 sheets defined 22.3% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.760A pdb=" N LYS H 64 " --> pdb=" O GLY H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'G' and resid 98 through 117 removed outlier: 4.038A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.572A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 122 through 126' Processing helix chain 'G' and resid 139 through 151 removed outlier: 3.529A pdb=" N ARG G 151 " --> pdb=" O ASP G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 350 Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.654A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 377 through 381 removed outlier: 3.580A pdb=" N GLY G 380 " --> pdb=" O ASN G 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 391 removed outlier: 3.788A pdb=" N PHE G 391 " --> pdb=" O SER G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 484 removed outlier: 4.064A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 521 Processing helix chain 'B' and resid 523 through 528 removed outlier: 3.586A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 542 removed outlier: 3.846A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 537 through 542' Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.543A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.828A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.828A pdb=" N TRP B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.510A pdb=" N LEU B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.832A pdb=" N LYS C 64 " --> pdb=" O GLY C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.999A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.538A pdb=" N LEU D 125 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS D 126 " --> pdb=" O THR D 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 126' Processing helix chain 'D' and resid 139 through 151 removed outlier: 3.529A pdb=" N ARG D 151 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 350 Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.635A pdb=" N THR D 373 " --> pdb=" O LEU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 381 removed outlier: 3.569A pdb=" N GLY D 380 " --> pdb=" O ASN D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.815A pdb=" N PHE D 391 " --> pdb=" O SER D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 484 removed outlier: 4.040A pdb=" N ASN D 478 " --> pdb=" O ASP D 474 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP D 479 " --> pdb=" O MET D 475 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 521 Processing helix chain 'E' and resid 523 through 528 removed outlier: 3.654A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 537 through 542 removed outlier: 3.906A pdb=" N ALA E 541 " --> pdb=" O LEU E 537 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG E 542 " --> pdb=" O THR E 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 537 through 542' Processing helix chain 'E' and resid 543 through 545 No H-bonds generated for 'chain 'E' and resid 543 through 545' Processing helix chain 'E' and resid 572 through 596 removed outlier: 3.527A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 615 Processing helix chain 'E' and resid 619 through 624 removed outlier: 3.820A pdb=" N ASP E 624 " --> pdb=" O SER E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.761A pdb=" N TRP E 631 " --> pdb=" O THR E 627 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS E 633 " --> pdb=" O LEU E 629 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE E 635 " --> pdb=" O TRP E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 662 removed outlier: 3.540A pdb=" N LEU E 646 " --> pdb=" O ILE E 642 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU E 647 " --> pdb=" O TYR E 643 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLU E 648 " --> pdb=" O GLY E 644 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.615A pdb=" N LYS I 64 " --> pdb=" O GLY I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 98 through 117 removed outlier: 4.012A pdb=" N GLU J 102 " --> pdb=" O ASN J 98 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE J 109 " --> pdb=" O HIS J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 126 removed outlier: 3.569A pdb=" N LEU J 125 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS J 126 " --> pdb=" O THR J 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 122 through 126' Processing helix chain 'J' and resid 139 through 151 Processing helix chain 'J' and resid 334 through 350 Processing helix chain 'J' and resid 368 through 373 removed outlier: 3.819A pdb=" N THR J 373 " --> pdb=" O LEU J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 381 removed outlier: 3.601A pdb=" N GLY J 380 " --> pdb=" O ASN J 377 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 391 removed outlier: 3.825A pdb=" N PHE J 391 " --> pdb=" O SER J 388 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 484 removed outlier: 4.047A pdb=" N ASN J 478 " --> pdb=" O ASP J 474 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRP J 479 " --> pdb=" O MET J 475 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU J 482 " --> pdb=" O ASN J 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 517 through 521 Processing helix chain 'K' and resid 523 through 528 removed outlier: 3.579A pdb=" N GLY K 527 " --> pdb=" O GLY K 524 " (cutoff:3.500A) Processing helix chain 'K' and resid 529 through 534 removed outlier: 3.515A pdb=" N SER K 534 " --> pdb=" O MET K 530 " (cutoff:3.500A) Processing helix chain 'K' and resid 537 through 542 removed outlier: 3.809A pdb=" N ALA K 541 " --> pdb=" O LEU K 537 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG K 542 " --> pdb=" O THR K 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 537 through 542' Processing helix chain 'K' and resid 543 through 545 No H-bonds generated for 'chain 'K' and resid 543 through 545' Processing helix chain 'K' and resid 572 through 596 removed outlier: 3.537A pdb=" N ASP K 589 " --> pdb=" O ARG K 585 " (cutoff:3.500A) Processing helix chain 'K' and resid 611 through 615 Processing helix chain 'K' and resid 618 through 624 removed outlier: 3.816A pdb=" N ASP K 624 " --> pdb=" O SER K 620 " (cutoff:3.500A) Processing helix chain 'K' and resid 627 through 636 removed outlier: 3.686A pdb=" N TRP K 631 " --> pdb=" O THR K 627 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS K 633 " --> pdb=" O LEU K 629 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU K 634 " --> pdb=" O GLN K 630 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE K 635 " --> pdb=" O TRP K 631 " (cutoff:3.500A) Processing helix chain 'K' and resid 638 through 662 removed outlier: 3.572A pdb=" N LEU K 646 " --> pdb=" O ILE K 642 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU K 647 " --> pdb=" O TYR K 643 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU K 648 " --> pdb=" O GLY K 644 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.522A pdb=" N THR L 5 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.875A pdb=" N ILE L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU L 37 " --> pdb=" O ARG L 46 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ARG L 46 " --> pdb=" O LEU L 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.573A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 9 through 10 removed outlier: 3.936A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 495 through 499 Processing sheet with id=AA6, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.907A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AA9, first strand: chain 'G' and resid 181 through 182 Processing sheet with id=AB1, first strand: chain 'G' and resid 202 through 203 removed outlier: 7.326A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 259 through 261 removed outlier: 4.380A pdb=" N GLY G 451 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.318A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.424A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.336A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 284 through 298 current: chain 'G' and resid 360 through 361 Processing sheet with id=AB3, first strand: chain 'G' and resid 271 through 273 removed outlier: 7.140A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.336A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.424A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.318A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 443 through 456 current: chain 'G' and resid 416 through 420 Processing sheet with id=AB4, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.922A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 4 through 5 removed outlier: 3.511A pdb=" N THR A 5 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 21 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 10 through 11 removed outlier: 3.878A pdb=" N ILE A 85 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU A 37 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ARG A 46 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.512A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET C 20 " --> pdb=" O MET C 80 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 9 through 10 removed outlier: 3.875A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N TRP C 47 " --> pdb=" O LYS C 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 495 through 499 removed outlier: 3.509A pdb=" N CYS E 604 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 45 through 46 removed outlier: 3.928A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'D' and resid 130 through 133 Processing sheet with id=AC4, first strand: chain 'D' and resid 181 through 182 Processing sheet with id=AC5, first strand: chain 'D' and resid 202 through 203 removed outlier: 7.341A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 259 through 261 removed outlier: 4.367A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.325A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.826A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.383A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS D 330 " --> pdb=" O THR D 297 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 271 through 273 removed outlier: 7.138A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 10.383A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.826A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.325A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D 359 " --> pdb=" O TRP D 395 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 304 through 312 removed outlier: 6.956A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.609A pdb=" N THR F 5 " --> pdb=" O LYS F 24 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE F 21 " --> pdb=" O LEU F 73 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.868A pdb=" N ILE F 85 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU F 37 " --> pdb=" O ARG F 46 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ARG F 46 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.532A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 9 through 10 removed outlier: 3.989A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TRP I 47 " --> pdb=" O LYS I 38 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP I 50 " --> pdb=" O ASN I 58 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 495 through 499 removed outlier: 5.137A pdb=" N VAL J 36 " --> pdb=" O THR K 606 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR K 606 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS K 604 " --> pdb=" O VAL J 38 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 45 through 46 removed outlier: 3.511A pdb=" N ILE J 84 " --> pdb=" O THR J 244 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'J' and resid 130 through 133 Processing sheet with id=AD8, first strand: chain 'J' and resid 181 through 182 Processing sheet with id=AD9, first strand: chain 'J' and resid 202 through 203 removed outlier: 6.971A pdb=" N THR J 202 " --> pdb=" O TYR J 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 259 through 261 removed outlier: 4.385A pdb=" N GLY J 451 " --> pdb=" O LEU J 260 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N ARG J 444 " --> pdb=" O ILE J 294 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE J 294 " --> pdb=" O ARG J 444 " (cutoff:3.500A) removed outlier: 9.823A pdb=" N VAL J 446 " --> pdb=" O VAL J 292 " (cutoff:3.500A) removed outlier: 10.748A pdb=" N VAL J 292 " --> pdb=" O VAL J 446 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N ASN J 448 " --> pdb=" O THR J 290 " (cutoff:3.500A) removed outlier: 10.330A pdb=" N THR J 290 " --> pdb=" O ASN J 448 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N THR J 450 " --> pdb=" O PHE J 288 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS J 330 " --> pdb=" O THR J 297 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 271 through 273 removed outlier: 7.133A pdb=" N THR J 450 " --> pdb=" O PHE J 288 " (cutoff:3.500A) removed outlier: 10.330A pdb=" N THR J 290 " --> pdb=" O ASN J 448 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N ASN J 448 " --> pdb=" O THR J 290 " (cutoff:3.500A) removed outlier: 10.748A pdb=" N VAL J 292 " --> pdb=" O VAL J 446 " (cutoff:3.500A) removed outlier: 9.823A pdb=" N VAL J 446 " --> pdb=" O VAL J 292 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE J 294 " --> pdb=" O ARG J 444 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N ARG J 444 " --> pdb=" O ILE J 294 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG J 360 " --> pdb=" O PHE J 468 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER J 393 " --> pdb=" O PHE J 361 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 304 through 312 removed outlier: 6.884A pdb=" N GLN J 315 " --> pdb=" O ILE J 309 " (cutoff:3.500A) 593 hydrogen bonds defined for protein. 1470 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.20 Time building geometry restraints manager: 9.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4681 1.33 - 1.46: 5583 1.46 - 1.58: 10220 1.58 - 1.71: 0 1.71 - 1.83: 174 Bond restraints: 20658 Sorted by residual: bond pdb=" C GLU C 100B" pdb=" N PRO C 100C" ideal model delta sigma weight residual 1.334 1.359 -0.025 8.40e-03 1.42e+04 8.82e+00 bond pdb=" C GLY I 53 " pdb=" N SER I 54 " ideal model delta sigma weight residual 1.335 1.304 0.031 1.35e-02 5.49e+03 5.24e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.50e+00 bond pdb=" C1 NAG b 1 " pdb=" O5 NAG b 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.36e+00 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.18e+00 ... (remaining 20653 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.54: 494 106.54 - 113.42: 11995 113.42 - 120.29: 6628 120.29 - 127.16: 8675 127.16 - 134.03: 264 Bond angle restraints: 28056 Sorted by residual: angle pdb=" C LEU C 82 " pdb=" N SER C 82A" pdb=" CA SER C 82A" ideal model delta sigma weight residual 121.70 131.12 -9.42 1.80e+00 3.09e-01 2.74e+01 angle pdb=" C LEU H 82 " pdb=" N SER H 82A" pdb=" CA SER H 82A" ideal model delta sigma weight residual 121.70 131.12 -9.42 1.80e+00 3.09e-01 2.74e+01 angle pdb=" C LEU I 82 " pdb=" N SER I 82A" pdb=" CA SER I 82A" ideal model delta sigma weight residual 121.70 131.10 -9.40 1.80e+00 3.09e-01 2.73e+01 angle pdb=" N ILE J 309 " pdb=" CA ILE J 309 " pdb=" C ILE J 309 " ideal model delta sigma weight residual 112.96 109.51 3.45 1.00e+00 1.00e+00 1.19e+01 angle pdb=" CA GLN K 652 " pdb=" CB GLN K 652 " pdb=" CG GLN K 652 " ideal model delta sigma weight residual 114.10 120.13 -6.03 2.00e+00 2.50e-01 9.08e+00 ... (remaining 28051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.16: 12019 22.16 - 44.33: 1139 44.33 - 66.49: 217 66.49 - 88.65: 103 88.65 - 110.82: 58 Dihedral angle restraints: 13536 sinusoidal: 6579 harmonic: 6957 Sorted by residual: dihedral pdb=" CB CYS J 201 " pdb=" SG CYS J 201 " pdb=" SG CYS J 433 " pdb=" CB CYS J 433 " ideal model delta sinusoidal sigma weight residual 93.00 29.92 63.08 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" CB CYS D 201 " pdb=" SG CYS D 201 " pdb=" SG CYS D 433 " pdb=" CB CYS D 433 " ideal model delta sinusoidal sigma weight residual 93.00 31.57 61.43 1 1.00e+01 1.00e-02 5.01e+01 dihedral pdb=" CB CYS G 201 " pdb=" SG CYS G 201 " pdb=" SG CYS G 433 " pdb=" CB CYS G 433 " ideal model delta sinusoidal sigma weight residual 93.00 31.71 61.29 1 1.00e+01 1.00e-02 4.99e+01 ... (remaining 13533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 3388 0.134 - 0.268: 26 0.268 - 0.402: 6 0.402 - 0.536: 0 0.536 - 0.670: 3 Chirality restraints: 3423 Sorted by residual: chirality pdb=" C1 NAG E 701 " pdb=" ND2 ASN E 611 " pdb=" C2 NAG E 701 " pdb=" O5 NAG E 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" C1 NAG K 701 " pdb=" ND2 ASN K 611 " pdb=" C2 NAG K 701 " pdb=" O5 NAG K 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" C1 NAG B 701 " pdb=" ND2 ASN B 611 " pdb=" C2 NAG B 701 " pdb=" O5 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.11e+01 ... (remaining 3420 not shown) Planarity restraints: 3501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 213 " 0.059 5.00e-02 4.00e+02 8.88e-02 1.26e+01 pdb=" N PRO D 214 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO D 214 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 214 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 213 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO G 214 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO G 214 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 214 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE J 213 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO J 214 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO J 214 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO J 214 " -0.032 5.00e-02 4.00e+02 ... (remaining 3498 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 330 2.64 - 3.20: 18788 3.20 - 3.77: 29634 3.77 - 4.33: 40102 4.33 - 4.90: 65069 Nonbonded interactions: 153923 Sorted by model distance: nonbonded pdb=" OE2 GLU J 275 " pdb=" NZ LYS J 282 " model vdw 2.069 2.520 nonbonded pdb=" O3 NAG a 1 " pdb=" O5 NAG a 2 " model vdw 2.131 2.440 nonbonded pdb=" O3 NAG T 1 " pdb=" O5 NAG T 2 " model vdw 2.131 2.440 nonbonded pdb=" O3 NAG M 1 " pdb=" O5 NAG M 2 " model vdw 2.132 2.440 nonbonded pdb=" O ASN G 377 " pdb=" ND2 ASN G 377 " model vdw 2.167 2.520 ... (remaining 153918 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 'F' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'e' selection = chain 'f' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'S' selection = chain 'Z' selection = chain 'g' } 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: 1.550 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: 6.050 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 52.540 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 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 : 0.004 0.057 20658 Z= 0.253 Angle : 0.683 9.425 28056 Z= 0.311 Chirality : 0.052 0.670 3423 Planarity : 0.004 0.089 3444 Dihedral : 19.301 110.817 8940 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.79 % Favored : 95.09 % Rotamer: Outliers : 0.09 % Allowed : 22.73 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.18), residues: 2382 helix: 1.64 (0.31), residues: 324 sheet: -0.58 (0.20), residues: 690 loop : -0.88 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 100D HIS 0.006 0.000 HIS D 85 PHE 0.016 0.001 PHE D 391 TYR 0.030 0.001 TYR J 435 ARG 0.010 0.000 ARG J 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 275 time to evaluate : 2.051 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: L 21 ILE cc_start: 0.7425 (pt) cc_final: 0.7076 (mm) REVERT: L 77 ARG cc_start: 0.8217 (mtp-110) cc_final: 0.8011 (ttp-170) REVERT: L 81 GLU cc_start: 0.8497 (mp0) cc_final: 0.8214 (mp0) REVERT: H 32 TYR cc_start: 0.8456 (m-80) cc_final: 0.8151 (m-80) REVERT: G 259 LEU cc_start: 0.7891 (mp) cc_final: 0.7618 (mp) REVERT: C 34 ILE cc_start: 0.8704 (mm) cc_final: 0.8222 (mm) REVERT: C 91 TYR cc_start: 0.6373 (m-10) cc_final: 0.6132 (m-10) REVERT: E 639 THR cc_start: 0.7489 (m) cc_final: 0.6777 (t) REVERT: F 21 ILE cc_start: 0.8650 (pt) cc_final: 0.8350 (mm) REVERT: I 45 LEU cc_start: 0.7222 (mm) cc_final: 0.6764 (mm) REVERT: I 51 ILE cc_start: 0.8040 (tp) cc_final: 0.7565 (tp) outliers start: 2 outliers final: 0 residues processed: 277 average time/residue: 0.3532 time to fit residues: 144.7120 Evaluate side-chains 146 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 114 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 chunk 217 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 GLN G 99 ASN G 330 HIS A 17 GLN C 81 GLN D 85 HIS ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 HIS I 81 GLN ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 103 GLN J 330 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20658 Z= 0.225 Angle : 0.691 11.187 28056 Z= 0.342 Chirality : 0.050 0.511 3423 Planarity : 0.005 0.083 3444 Dihedral : 12.415 73.108 4515 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.72 % Favored : 93.16 % Rotamer: Outliers : 0.05 % Allowed : 3.98 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.18), residues: 2382 helix: 1.44 (0.29), residues: 351 sheet: -0.72 (0.18), residues: 753 loop : -0.98 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP K 571 HIS 0.005 0.001 HIS D 85 PHE 0.021 0.002 PHE D 159 TYR 0.027 0.002 TYR I 91 ARG 0.005 0.001 ARG J 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 206 time to evaluate : 2.277 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: L 27 ASP cc_start: 0.7792 (t0) cc_final: 0.7522 (t70) REVERT: L 74 LYS cc_start: 0.8772 (mmpt) cc_final: 0.8516 (mmmt) REVERT: H 32 TYR cc_start: 0.8495 (m-80) cc_final: 0.8132 (m-80) REVERT: B 535 MET cc_start: 0.8588 (mpp) cc_final: 0.8148 (mtm) REVERT: B 643 TYR cc_start: 0.8202 (m-10) cc_final: 0.7886 (m-10) REVERT: B 654 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7680 (mm-30) REVERT: C 34 ILE cc_start: 0.8563 (mm) cc_final: 0.8255 (mm) REVERT: D 475 MET cc_start: 0.6325 (mmm) cc_final: 0.6014 (mmm) REVERT: E 639 THR cc_start: 0.7886 (m) cc_final: 0.7156 (t) REVERT: E 643 TYR cc_start: 0.8110 (m-10) cc_final: 0.7893 (m-10) REVERT: F 21 ILE cc_start: 0.8619 (pt) cc_final: 0.8367 (mm) REVERT: F 74 LYS cc_start: 0.9086 (mmtm) cc_final: 0.8863 (mmmt) REVERT: I 5 GLN cc_start: 0.7576 (mm110) cc_final: 0.7315 (mm-40) REVERT: I 32 TYR cc_start: 0.8461 (m-80) cc_final: 0.7955 (m-80) outliers start: 1 outliers final: 0 residues processed: 207 average time/residue: 0.3446 time to fit residues: 108.0588 Evaluate side-chains 138 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 7.9990 chunk 67 optimal weight: 0.0050 chunk 181 optimal weight: 0.6980 chunk 148 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 218 optimal weight: 4.9990 chunk 235 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 216 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 17 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 GLN J 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20658 Z= 0.189 Angle : 0.640 9.265 28056 Z= 0.315 Chirality : 0.048 0.495 3423 Planarity : 0.004 0.048 3444 Dihedral : 9.675 59.715 4515 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.88 % Favored : 94.00 % Rotamer: Outliers : 0.09 % Allowed : 3.22 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.17), residues: 2382 helix: 1.26 (0.28), residues: 351 sheet: -0.74 (0.18), residues: 753 loop : -0.99 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 479 HIS 0.003 0.001 HIS L 93 PHE 0.013 0.001 PHE J 53 TYR 0.014 0.001 TYR A 86 ARG 0.005 0.000 ARG L 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 183 time to evaluate : 2.508 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: L 27 ASP cc_start: 0.7836 (t0) cc_final: 0.7529 (t70) REVERT: L 74 LYS cc_start: 0.8775 (mmpt) cc_final: 0.8360 (mmmt) REVERT: L 81 GLU cc_start: 0.8229 (mp0) cc_final: 0.7789 (mp0) REVERT: H 32 TYR cc_start: 0.8492 (m-80) cc_final: 0.8148 (m-80) REVERT: B 643 TYR cc_start: 0.8226 (m-10) cc_final: 0.7911 (m-80) REVERT: C 23 LYS cc_start: 0.8802 (tptt) cc_final: 0.8494 (tptp) REVERT: C 34 ILE cc_start: 0.8651 (mm) cc_final: 0.8295 (mm) REVERT: D 475 MET cc_start: 0.6161 (mmm) cc_final: 0.5923 (mmm) REVERT: F 4 MET cc_start: 0.5691 (mmm) cc_final: 0.5295 (mmp) REVERT: F 21 ILE cc_start: 0.8649 (pt) cc_final: 0.8416 (mm) REVERT: F 74 LYS cc_start: 0.9108 (mmtm) cc_final: 0.8901 (mmmt) REVERT: I 32 TYR cc_start: 0.8617 (m-80) cc_final: 0.8000 (m-80) REVERT: I 100 LEU cc_start: 0.8039 (mt) cc_final: 0.7793 (mt) REVERT: J 52 LEU cc_start: 0.8503 (mt) cc_final: 0.7844 (mp) REVERT: J 107 ASP cc_start: 0.7518 (t70) cc_final: 0.7289 (t70) outliers start: 2 outliers final: 0 residues processed: 184 average time/residue: 0.3300 time to fit residues: 93.4355 Evaluate side-chains 126 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 4.9990 chunk 164 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 24 optimal weight: 0.1980 chunk 104 optimal weight: 0.7980 chunk 146 optimal weight: 10.0000 chunk 219 optimal weight: 0.4980 chunk 231 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 17 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 HIS F 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20658 Z= 0.191 Angle : 0.612 9.303 28056 Z= 0.303 Chirality : 0.048 0.488 3423 Planarity : 0.004 0.042 3444 Dihedral : 7.717 59.153 4515 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.68 % Favored : 93.20 % Rotamer: Outliers : 0.09 % Allowed : 3.12 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.18), residues: 2382 helix: 1.44 (0.29), residues: 348 sheet: -0.71 (0.18), residues: 783 loop : -0.85 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 479 HIS 0.002 0.001 HIS J 216 PHE 0.012 0.001 PHE F 62 TYR 0.014 0.001 TYR E 643 ARG 0.004 0.000 ARG K 542 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 179 time to evaluate : 2.190 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: L 21 ILE cc_start: 0.7762 (pt) cc_final: 0.7376 (mm) REVERT: L 27 ASP cc_start: 0.7899 (t0) cc_final: 0.7586 (t70) REVERT: L 74 LYS cc_start: 0.8775 (mmpt) cc_final: 0.8345 (mmmt) REVERT: L 81 GLU cc_start: 0.8241 (mp0) cc_final: 0.7787 (mp0) REVERT: H 32 TYR cc_start: 0.8587 (m-80) cc_final: 0.8204 (m-80) REVERT: H 51 ILE cc_start: 0.8423 (tp) cc_final: 0.8181 (tp) REVERT: A 17 GLN cc_start: 0.4015 (OUTLIER) cc_final: 0.3755 (pp30) REVERT: C 23 LYS cc_start: 0.8815 (tptt) cc_final: 0.8538 (tptp) REVERT: C 34 ILE cc_start: 0.8668 (mm) cc_final: 0.8348 (mm) REVERT: E 595 ILE cc_start: 0.8885 (tp) cc_final: 0.8651 (tp) REVERT: F 4 MET cc_start: 0.5879 (mmm) cc_final: 0.5361 (mmp) REVERT: F 74 LYS cc_start: 0.9142 (mmtm) cc_final: 0.8873 (mmmt) REVERT: I 100 LEU cc_start: 0.8052 (mt) cc_final: 0.7741 (mt) REVERT: J 107 ASP cc_start: 0.7655 (t70) cc_final: 0.7310 (t70) outliers start: 2 outliers final: 0 residues processed: 181 average time/residue: 0.3063 time to fit residues: 87.3231 Evaluate side-chains 128 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 160 optimal weight: 40.0000 chunk 0 optimal weight: 30.0000 chunk 118 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 HIS G 348 GLN G 478 ASN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 618 ASN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 249 HIS J 348 GLN J 478 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20658 Z= 0.292 Angle : 0.685 9.397 28056 Z= 0.340 Chirality : 0.048 0.483 3423 Planarity : 0.004 0.043 3444 Dihedral : 7.126 56.857 4515 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.60 % Favored : 92.28 % Rotamer: Outliers : 0.09 % Allowed : 2.65 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.17), residues: 2382 helix: 1.12 (0.28), residues: 348 sheet: -0.92 (0.18), residues: 765 loop : -0.81 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 571 HIS 0.004 0.001 HIS D 249 PHE 0.027 0.002 PHE J 53 TYR 0.016 0.001 TYR G 217 ARG 0.003 0.000 ARG G 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 2.238 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: L 21 ILE cc_start: 0.7972 (pt) cc_final: 0.7529 (mm) REVERT: L 27 ASP cc_start: 0.8078 (t0) cc_final: 0.7740 (t70) REVERT: L 74 LYS cc_start: 0.8867 (mmpt) cc_final: 0.8448 (mmmt) REVERT: L 81 GLU cc_start: 0.8406 (mp0) cc_final: 0.8001 (mp0) REVERT: H 23 LYS cc_start: 0.8094 (tptp) cc_final: 0.7818 (tptp) REVERT: H 32 TYR cc_start: 0.8775 (m-80) cc_final: 0.8386 (m-80) REVERT: H 102 TYR cc_start: 0.6937 (m-10) cc_final: 0.6622 (m-10) REVERT: B 543 ASN cc_start: 0.7977 (t0) cc_final: 0.7776 (t0) REVERT: B 584 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7993 (tm-30) REVERT: B 643 TYR cc_start: 0.8243 (m-10) cc_final: 0.7788 (m-10) REVERT: C 23 LYS cc_start: 0.8892 (tptt) cc_final: 0.8600 (tptp) REVERT: C 32 TYR cc_start: 0.8188 (m-80) cc_final: 0.7662 (m-80) REVERT: C 34 ILE cc_start: 0.8677 (mm) cc_final: 0.8340 (mm) REVERT: D 95 MET cc_start: 0.7180 (ttm) cc_final: 0.6796 (ttm) REVERT: D 426 MET cc_start: 0.8401 (tpp) cc_final: 0.7870 (ttm) REVERT: E 543 ASN cc_start: 0.8241 (t0) cc_final: 0.8040 (t0) REVERT: E 595 ILE cc_start: 0.9054 (tp) cc_final: 0.8847 (tp) REVERT: F 21 ILE cc_start: 0.8802 (mm) cc_final: 0.8361 (pt) REVERT: F 74 LYS cc_start: 0.9195 (mmtm) cc_final: 0.8934 (mmmt) REVERT: I 5 GLN cc_start: 0.7567 (mm-40) cc_final: 0.7297 (mm-40) REVERT: I 23 LYS cc_start: 0.7948 (tptp) cc_final: 0.7741 (tptp) REVERT: J 95 MET cc_start: 0.7600 (ttp) cc_final: 0.7129 (ttp) REVERT: J 107 ASP cc_start: 0.7667 (t70) cc_final: 0.7269 (t70) REVERT: J 271 MET cc_start: 0.7787 (mmm) cc_final: 0.7522 (mmm) outliers start: 2 outliers final: 0 residues processed: 168 average time/residue: 0.3911 time to fit residues: 103.7615 Evaluate side-chains 122 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 57 optimal weight: 0.4980 chunk 232 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 107 optimal weight: 0.0670 chunk 19 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 overall best weight: 2.5124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20658 Z= 0.242 Angle : 0.640 9.448 28056 Z= 0.320 Chirality : 0.048 0.484 3423 Planarity : 0.004 0.040 3444 Dihedral : 6.772 56.541 4515 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.93 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.18), residues: 2382 helix: 1.65 (0.29), residues: 330 sheet: -1.00 (0.18), residues: 798 loop : -0.81 (0.19), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP J 479 HIS 0.004 0.001 HIS G 249 PHE 0.016 0.002 PHE J 383 TYR 0.024 0.002 TYR A 86 ARG 0.011 0.001 ARG J 503 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 2.501 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: L 21 ILE cc_start: 0.8038 (pt) cc_final: 0.7575 (mm) REVERT: L 27 ASP cc_start: 0.8112 (t0) cc_final: 0.7779 (t70) REVERT: L 74 LYS cc_start: 0.8873 (mmpt) cc_final: 0.8474 (mmmt) REVERT: L 81 GLU cc_start: 0.8429 (mp0) cc_final: 0.8033 (mp0) REVERT: H 23 LYS cc_start: 0.8055 (tptp) cc_final: 0.7817 (tptp) REVERT: H 32 TYR cc_start: 0.8709 (m-80) cc_final: 0.8280 (m-80) REVERT: H 102 TYR cc_start: 0.6888 (m-10) cc_final: 0.6639 (m-10) REVERT: B 535 MET cc_start: 0.8599 (mpp) cc_final: 0.8399 (mpp) REVERT: B 543 ASN cc_start: 0.8031 (t0) cc_final: 0.7793 (t0) REVERT: B 643 TYR cc_start: 0.8202 (m-10) cc_final: 0.7758 (m-10) REVERT: C 23 LYS cc_start: 0.8823 (tptt) cc_final: 0.8536 (tptp) REVERT: C 32 TYR cc_start: 0.8315 (m-80) cc_final: 0.7772 (m-80) REVERT: C 34 ILE cc_start: 0.8763 (mm) cc_final: 0.8431 (mm) REVERT: E 595 ILE cc_start: 0.9072 (tp) cc_final: 0.8870 (tp) REVERT: F 21 ILE cc_start: 0.8748 (mm) cc_final: 0.8291 (pt) REVERT: F 74 LYS cc_start: 0.9195 (mmtm) cc_final: 0.8952 (mmmt) REVERT: J 107 ASP cc_start: 0.7652 (t70) cc_final: 0.7256 (t70) REVERT: J 271 MET cc_start: 0.7763 (mmm) cc_final: 0.7495 (mmm) REVERT: J 426 MET cc_start: 0.8079 (ttm) cc_final: 0.7863 (ttm) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.3544 time to fit residues: 88.1019 Evaluate side-chains 119 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 9.9990 chunk 26 optimal weight: 0.0000 chunk 132 optimal weight: 10.0000 chunk 169 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 195 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 96 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN J 105 HIS J 203 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20658 Z= 0.190 Angle : 0.626 10.652 28056 Z= 0.312 Chirality : 0.047 0.473 3423 Planarity : 0.004 0.039 3444 Dihedral : 6.383 56.708 4515 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.97 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.18), residues: 2382 helix: 1.70 (0.29), residues: 312 sheet: -0.90 (0.18), residues: 798 loop : -0.71 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 35 HIS 0.003 0.001 HIS D 85 PHE 0.013 0.001 PHE D 376 TYR 0.013 0.001 TYR A 86 ARG 0.007 0.000 ARG K 542 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 2.327 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: L 21 ILE cc_start: 0.8088 (pt) cc_final: 0.7626 (mm) REVERT: L 27 ASP cc_start: 0.8079 (t0) cc_final: 0.7753 (t70) REVERT: L 74 LYS cc_start: 0.8885 (mmpt) cc_final: 0.8491 (mmmt) REVERT: L 81 GLU cc_start: 0.8429 (mp0) cc_final: 0.8038 (mp0) REVERT: H 32 TYR cc_start: 0.8682 (m-80) cc_final: 0.8233 (m-80) REVERT: H 102 TYR cc_start: 0.6825 (m-10) cc_final: 0.6608 (m-10) REVERT: B 535 MET cc_start: 0.8587 (mpp) cc_final: 0.8332 (mpp) REVERT: B 543 ASN cc_start: 0.7967 (t0) cc_final: 0.7744 (t0) REVERT: C 23 LYS cc_start: 0.8810 (tptt) cc_final: 0.8554 (tptp) REVERT: C 32 TYR cc_start: 0.8368 (m-80) cc_final: 0.7803 (m-80) REVERT: C 34 ILE cc_start: 0.8796 (mm) cc_final: 0.8483 (mm) REVERT: D 150 MET cc_start: 0.7142 (ppp) cc_final: 0.6925 (ppp) REVERT: E 595 ILE cc_start: 0.9026 (tp) cc_final: 0.8808 (tp) REVERT: F 21 ILE cc_start: 0.8745 (mm) cc_final: 0.8292 (pt) REVERT: F 54 LEU cc_start: 0.8030 (mt) cc_final: 0.7746 (tt) REVERT: F 74 LYS cc_start: 0.9214 (mmtm) cc_final: 0.8937 (mmmt) REVERT: I 5 GLN cc_start: 0.7528 (mm-40) cc_final: 0.7026 (mm-40) REVERT: J 107 ASP cc_start: 0.7682 (t70) cc_final: 0.7352 (t70) REVERT: J 109 ILE cc_start: 0.8933 (mt) cc_final: 0.8648 (mt) REVERT: J 271 MET cc_start: 0.7717 (mmm) cc_final: 0.7510 (mmm) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.3531 time to fit residues: 90.8836 Evaluate side-chains 119 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 147 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 181 optimal weight: 10.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 618 ASN F 96 GLN J 283 ASN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 616 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20658 Z= 0.317 Angle : 0.687 10.352 28056 Z= 0.343 Chirality : 0.048 0.474 3423 Planarity : 0.004 0.044 3444 Dihedral : 6.662 56.805 4515 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.89 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.18), residues: 2382 helix: 1.46 (0.29), residues: 315 sheet: -1.00 (0.18), residues: 828 loop : -0.68 (0.19), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 35 HIS 0.005 0.001 HIS D 374 PHE 0.018 0.002 PHE G 383 TYR 0.015 0.002 TYR A 86 ARG 0.007 0.001 ARG K 542 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 2.342 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: L 27 ASP cc_start: 0.8085 (t0) cc_final: 0.7817 (t70) REVERT: L 74 LYS cc_start: 0.8906 (mmpt) cc_final: 0.8538 (mmmt) REVERT: L 81 GLU cc_start: 0.8534 (mp0) cc_final: 0.8124 (mp0) REVERT: H 32 TYR cc_start: 0.8830 (m-80) cc_final: 0.8402 (m-80) REVERT: B 535 MET cc_start: 0.8687 (mpp) cc_final: 0.8438 (mpp) REVERT: B 584 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7895 (tm-30) REVERT: C 23 LYS cc_start: 0.8837 (tptt) cc_final: 0.8613 (tptp) REVERT: C 32 TYR cc_start: 0.8557 (m-80) cc_final: 0.7929 (m-80) REVERT: C 34 ILE cc_start: 0.8850 (mm) cc_final: 0.8531 (mm) REVERT: D 150 MET cc_start: 0.7289 (ppp) cc_final: 0.7040 (ppp) REVERT: D 426 MET cc_start: 0.8318 (tpp) cc_final: 0.8012 (tpp) REVERT: E 595 ILE cc_start: 0.9096 (tp) cc_final: 0.8846 (tp) REVERT: F 21 ILE cc_start: 0.8782 (mm) cc_final: 0.8349 (pt) REVERT: F 74 LYS cc_start: 0.9212 (mmtm) cc_final: 0.8949 (mmmt) REVERT: J 107 ASP cc_start: 0.7758 (t70) cc_final: 0.7443 (t70) REVERT: J 271 MET cc_start: 0.7785 (mmm) cc_final: 0.7463 (mmm) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.3436 time to fit residues: 80.7741 Evaluate side-chains 108 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 214 optimal weight: 0.1980 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20658 Z= 0.210 Angle : 0.640 9.408 28056 Z= 0.319 Chirality : 0.047 0.463 3423 Planarity : 0.004 0.040 3444 Dihedral : 6.378 56.576 4515 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.68 % Favored : 93.16 % Rotamer: Outliers : 0.05 % Allowed : 0.71 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.18), residues: 2382 helix: 1.68 (0.30), residues: 315 sheet: -0.95 (0.18), residues: 828 loop : -0.61 (0.19), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP J 479 HIS 0.003 0.001 HIS G 374 PHE 0.020 0.001 PHE L 62 TYR 0.018 0.001 TYR K 638 ARG 0.007 0.000 ARG F 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 2.279 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: L 21 ILE cc_start: 0.8177 (pt) cc_final: 0.7657 (mm) REVERT: L 27 ASP cc_start: 0.8020 (t0) cc_final: 0.7735 (t70) REVERT: L 74 LYS cc_start: 0.8956 (mmpt) cc_final: 0.8579 (mmmt) REVERT: L 81 GLU cc_start: 0.8540 (mp0) cc_final: 0.8159 (mp0) REVERT: H 32 TYR cc_start: 0.8709 (m-80) cc_final: 0.8321 (m-80) REVERT: B 535 MET cc_start: 0.8675 (mpp) cc_final: 0.8406 (mpp) REVERT: C 23 LYS cc_start: 0.8816 (tptt) cc_final: 0.8565 (tptp) REVERT: C 32 TYR cc_start: 0.8505 (m-80) cc_final: 0.8020 (m-80) REVERT: C 34 ILE cc_start: 0.8862 (mm) cc_final: 0.8541 (mm) REVERT: D 125 LEU cc_start: 0.8612 (mt) cc_final: 0.8407 (mt) REVERT: D 150 MET cc_start: 0.7255 (ppp) cc_final: 0.6871 (ppp) REVERT: E 595 ILE cc_start: 0.9058 (tp) cc_final: 0.8820 (tp) REVERT: F 21 ILE cc_start: 0.8766 (mm) cc_final: 0.8299 (pt) REVERT: F 74 LYS cc_start: 0.9199 (mmtm) cc_final: 0.8953 (mmmt) REVERT: J 107 ASP cc_start: 0.7736 (t70) cc_final: 0.7345 (t70) REVERT: J 109 ILE cc_start: 0.9004 (mt) cc_final: 0.8518 (mt) REVERT: J 271 MET cc_start: 0.7728 (mmm) cc_final: 0.7438 (mmm) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.3259 time to fit residues: 77.1224 Evaluate side-chains 111 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 8.9990 chunk 227 optimal weight: 0.0020 chunk 139 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 239 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 19 optimal weight: 20.0000 chunk 147 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 overall best weight: 1.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20658 Z= 0.209 Angle : 0.639 10.322 28056 Z= 0.317 Chirality : 0.047 0.461 3423 Planarity : 0.004 0.058 3444 Dihedral : 6.238 56.858 4515 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.88 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.18), residues: 2382 helix: 1.49 (0.29), residues: 333 sheet: -0.89 (0.18), residues: 828 loop : -0.61 (0.19), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP G 479 HIS 0.003 0.001 HIS D 85 PHE 0.013 0.001 PHE J 383 TYR 0.019 0.001 TYR K 638 ARG 0.008 0.000 ARG L 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4764 Ramachandran restraints generated. 2382 Oldfield, 0 Emsley, 2382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.461 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: L 21 ILE cc_start: 0.8139 (pt) cc_final: 0.7626 (mm) REVERT: L 27 ASP cc_start: 0.8025 (t0) cc_final: 0.7738 (t70) REVERT: L 74 LYS cc_start: 0.8959 (mmpt) cc_final: 0.8587 (mmmt) REVERT: L 81 GLU cc_start: 0.8543 (mp0) cc_final: 0.8135 (mp0) REVERT: H 23 LYS cc_start: 0.8094 (tptp) cc_final: 0.7861 (tptp) REVERT: H 32 TYR cc_start: 0.8688 (m-80) cc_final: 0.8376 (m-80) REVERT: B 535 MET cc_start: 0.8740 (mpp) cc_final: 0.8410 (mpp) REVERT: C 23 LYS cc_start: 0.8832 (tptt) cc_final: 0.8573 (tptp) REVERT: C 32 TYR cc_start: 0.8514 (m-80) cc_final: 0.8000 (m-80) REVERT: C 34 ILE cc_start: 0.8870 (mm) cc_final: 0.8559 (mm) REVERT: D 150 MET cc_start: 0.7290 (ppp) cc_final: 0.7056 (ppp) REVERT: E 595 ILE cc_start: 0.9067 (tp) cc_final: 0.8828 (tp) REVERT: F 21 ILE cc_start: 0.8844 (mm) cc_final: 0.8417 (pt) REVERT: F 74 LYS cc_start: 0.9192 (mmtm) cc_final: 0.8957 (mmmt) REVERT: I 51 ILE cc_start: 0.8499 (tp) cc_final: 0.8296 (tp) REVERT: J 107 ASP cc_start: 0.7721 (t70) cc_final: 0.7348 (t70) REVERT: J 271 MET cc_start: 0.7766 (mmm) cc_final: 0.7458 (mmm) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3415 time to fit residues: 82.9034 Evaluate side-chains 115 residues out of total 2115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 175 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 190 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 195 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN C 3 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 618 ASN F 96 GLN ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.063428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.045577 restraints weight = 104900.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.047796 restraints weight = 60165.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.048435 restraints weight = 37523.234| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 20658 Z= 0.399 Angle : 0.776 12.516 28056 Z= 0.384 Chirality : 0.049 0.470 3423 Planarity : 0.004 0.040 3444 Dihedral : 7.091 56.961 4515 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.61 % Favored : 91.18 % Rotamer: Outliers : 0.05 % Allowed : 0.43 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.18), residues: 2382 helix: 1.06 (0.29), residues: 333 sheet: -0.92 (0.18), residues: 807 loop : -0.83 (0.19), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP G 479 HIS 0.007 0.001 HIS D 85 PHE 0.030 0.002 PHE D 361 TYR 0.026 0.002 TYR K 643 ARG 0.021 0.001 ARG F 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3225.49 seconds wall clock time: 61 minutes 16.53 seconds (3676.53 seconds total)