Starting phenix.real_space_refine on Mon Mar 18 17:13:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k37_22652/03_2024/7k37_22652.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k37_22652/03_2024/7k37_22652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k37_22652/03_2024/7k37_22652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k37_22652/03_2024/7k37_22652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k37_22652/03_2024/7k37_22652.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k37_22652/03_2024/7k37_22652.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 99 5.16 5 C 13452 2.51 5 N 3639 2.21 5 O 4371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 101": "OD1" <-> "OD2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 101": "OD1" <-> "OD2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 280": "OE1" <-> "OE2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D GLU 165": "OE1" <-> "OE2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 101": "OD1" <-> "OD2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "E TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 280": "OE1" <-> "OE2" Residue "F GLU 15": "OE1" <-> "OE2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F GLU 67": "OE1" <-> "OE2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F ARG 124": "NH1" <-> "NH2" Residue "F GLU 165": "OE1" <-> "OE2" Residue "G ARG 17": "NH1" <-> "NH2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 17": "NH1" <-> "NH2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J GLU 82": "OE1" <-> "OE2" Residue "J ARG 98": "NH1" <-> "NH2" Residue "J PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 113": "NH1" <-> "NH2" Residue "K PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 166": "OE1" <-> "OE2" Residue "K PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 46": "OE1" <-> "OE2" Residue "L GLU 82": "OE1" <-> "OE2" Residue "L ARG 98": "NH1" <-> "NH2" Residue "L PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21561 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "B" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1398 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "C" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "D" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1398 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "E" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "F" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1398 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "G" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "H" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "I" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "J" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "K" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "L" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.73, per 1000 atoms: 0.64 Number of scatterers: 21561 At special positions: 0 Unit cell: (184.87, 184.87, 146.3, 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 99 16.00 O 4371 8.00 N 3639 7.00 C 13452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.11 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=1.95 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.04 Simple disulfide: pdb=" SG CYS G 139 " - pdb=" SG CYS G 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.04 Simple disulfide: pdb=" SG CYS I 139 " - pdb=" SG CYS I 199 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 150 " - pdb=" SG CYS J 206 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.04 Simple disulfide: pdb=" SG CYS K 139 " - pdb=" SG CYS K 199 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 150 " - pdb=" SG CYS L 206 " 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 ALPHA1-2 " MAN O 5 " - " MAN O 6 " " MAN R 5 " - " MAN R 6 " " MAN U 5 " - " MAN U 6 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 8 " " MAN O 4 " - " MAN O 7 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 8 " " MAN R 4 " - " MAN R 7 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 8 " " MAN U 4 " - " MAN U 7 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 4 " " MAN O 4 " - " MAN O 5 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 4 " " MAN R 4 " - " MAN R 5 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A 401 " - " ASN A 22 " " NAG A 402 " - " ASN A 81 " " NAG B 301 " - " ASN B 154 " " NAG C 401 " - " ASN C 22 " " NAG C 402 " - " ASN C 81 " " NAG D 301 " - " ASN D 154 " " NAG E 401 " - " ASN E 22 " " NAG E 402 " - " ASN E 81 " " NAG F 301 " - " ASN F 154 " " NAG M 1 " - " ASN A 38 " " NAG N 1 " - " ASN A 165 " " NAG O 1 " - " ASN A 285 " " NAG P 1 " - " ASN C 38 " " NAG Q 1 " - " ASN C 165 " " NAG R 1 " - " ASN C 285 " " NAG S 1 " - " ASN E 38 " " NAG T 1 " - " ASN E 165 " " NAG U 1 " - " ASN E 285 " Time building additional restraints: 8.95 Conformation dependent library (CDL) restraints added in 4.0 seconds 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4962 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 65 sheets defined 19.1% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 5.201A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 38 through 50 removed outlier: 4.462A pdb=" N GLY B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 126 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 158 through 161 removed outlier: 3.542A pdb=" N VAL B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 158 through 161' Processing helix chain 'B' and resid 162 through 172 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 5.201A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'D' and resid 38 through 50 removed outlier: 4.463A pdb=" N GLY D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 126 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 158 through 161 removed outlier: 3.541A pdb=" N VAL D 161 " --> pdb=" O ASP D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 158 through 161' Processing helix chain 'D' and resid 162 through 172 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 5.201A pdb=" N VAL E 78 " --> pdb=" O HIS E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 116 Processing helix chain 'E' and resid 187 through 195 Processing helix chain 'F' and resid 38 through 50 removed outlier: 4.463A pdb=" N GLY F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 126 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 158 through 161 removed outlier: 3.541A pdb=" N VAL F 161 " --> pdb=" O ASP F 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 158 through 161' Processing helix chain 'F' and resid 162 through 172 Processing helix chain 'G' and resid 126 through 132 Processing helix chain 'G' and resid 187 through 192 removed outlier: 3.778A pdb=" N GLU G 192 " --> pdb=" O LYS G 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 195 through 202 removed outlier: 4.516A pdb=" N GLY H 200 " --> pdb=" O SER H 196 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR H 201 " --> pdb=" O SER H 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 85 Processing helix chain 'I' and resid 126 through 132 Processing helix chain 'I' and resid 188 through 192 removed outlier: 3.521A pdb=" N GLU I 192 " --> pdb=" O LYS I 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 188 through 192' Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 106 through 110 Processing helix chain 'J' and resid 195 through 202 removed outlier: 4.517A pdb=" N GLY J 200 " --> pdb=" O SER J 196 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR J 201 " --> pdb=" O SER J 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'K' and resid 126 through 132 removed outlier: 3.817A pdb=" N LEU K 130 " --> pdb=" O SER K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 194 Processing helix chain 'L' and resid 28 through 32 Processing helix chain 'L' and resid 62 through 65 Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'L' and resid 106 through 110 Processing helix chain 'L' and resid 195 through 202 removed outlier: 4.518A pdb=" N GLY L 200 " --> pdb=" O SER L 196 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR L 201 " --> pdb=" O SER L 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 13 through 14 removed outlier: 8.132A pdb=" N TRP B 14 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N HIS A 17 " --> pdb=" O TRP B 14 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR B 22 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 14 removed outlier: 8.132A pdb=" N TRP B 14 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N HIS A 17 " --> pdb=" O TRP B 14 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA4, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA5, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.012A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A 53 " --> pdb=" O CYS A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 101 removed outlier: 6.876A pdb=" N ASP A 101 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 100 through 101 removed outlier: 6.876A pdb=" N ASP A 101 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB2, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.725A pdb=" N ALA A 138 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N GLY A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB4, first strand: chain 'A' and resid 286 through 288 removed outlier: 4.189A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 33 through 37 removed outlier: 4.744A pdb=" N TYR D 22 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AB7, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB8, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB9, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.012A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 58 through 61 Processing sheet with id=AC2, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.876A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.876A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC5, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.726A pdb=" N ALA C 138 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 10.803A pdb=" N GLY C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC7, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.189A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 13 through 14 removed outlier: 8.175A pdb=" N TRP F 14 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N HIS E 17 " --> pdb=" O TRP F 14 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR F 22 " --> pdb=" O ASP F 37 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 13 through 14 removed outlier: 8.175A pdb=" N TRP F 14 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N HIS E 17 " --> pdb=" O TRP F 14 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AD2, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD3, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD4, first strand: chain 'E' and resid 51 through 54 removed outlier: 6.013A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS E 277 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN E 53 " --> pdb=" O CYS E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 58 through 61 Processing sheet with id=AD6, first strand: chain 'E' and resid 100 through 101 removed outlier: 6.877A pdb=" N ASP E 101 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N TRP E 234 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 100 through 101 removed outlier: 6.877A pdb=" N ASP E 101 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N TRP E 234 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD9, first strand: chain 'E' and resid 136 through 141 removed outlier: 7.726A pdb=" N ALA E 138 " --> pdb=" O GLY E 144 " (cutoff:3.500A) removed outlier: 10.804A pdb=" N GLY E 144 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AE2, first strand: chain 'E' and resid 286 through 288 removed outlier: 4.190A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.538A pdb=" N THR G 109 " --> pdb=" O VAL G 10 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AE5, first strand: chain 'G' and resid 119 through 123 removed outlier: 3.557A pdb=" N PHE G 123 " --> pdb=" O VAL G 138 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL G 138 " --> pdb=" O PHE G 123 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N TYR G 178 " --> pdb=" O ASN G 143 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER G 179 " --> pdb=" O THR G 169 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 149 through 155 removed outlier: 4.127A pdb=" N LYS G 150 " --> pdb=" O THR G 202 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR G 197 " --> pdb=" O PHE G 214 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.668A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TRP H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.668A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 130 through 134 removed outlier: 5.918A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 160 through 164 Processing sheet with id=AF3, first strand: chain 'I' and resid 4 through 5 removed outlier: 3.840A pdb=" N THR I 5 " --> pdb=" O THR I 23 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.460A pdb=" N TRP I 37 " --> pdb=" O LEU I 49 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 119 through 123 removed outlier: 3.743A pdb=" N VAL I 138 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TYR I 178 " --> pdb=" O ASN I 143 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER I 179 " --> pdb=" O THR I 169 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 150 through 154 Processing sheet with id=AF7, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AF8, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.669A pdb=" N GLU J 10 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TRP J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.669A pdb=" N GLU J 10 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL J 115 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 130 through 134 removed outlier: 5.919A pdb=" N TYR J 186 " --> pdb=" O ASP J 154 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 160 through 164 Processing sheet with id=AG3, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.615A pdb=" N THR K 109 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY K 12 " --> pdb=" O THR K 109 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP K 37 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AG5, first strand: chain 'K' and resid 119 through 123 removed outlier: 3.736A pdb=" N PHE K 123 " --> pdb=" O VAL K 138 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL K 138 " --> pdb=" O PHE K 123 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER K 136 " --> pdb=" O LEU K 186 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU K 186 " --> pdb=" O SER K 136 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N VAL K 138 " --> pdb=" O LEU K 184 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU K 184 " --> pdb=" O VAL K 138 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LEU K 140 " --> pdb=" O SER K 182 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER K 182 " --> pdb=" O LEU K 140 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ASN K 142 " --> pdb=" O LEU K 180 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU K 180 " --> pdb=" O ASN K 142 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 158 through 159 removed outlier: 3.565A pdb=" N LYS K 150 " --> pdb=" O THR K 202 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR K 202 " --> pdb=" O LYS K 150 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AG8, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.668A pdb=" N GLU L 10 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU L 34 " --> pdb=" O TRP L 50 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TRP L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.668A pdb=" N GLU L 10 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL L 115 " --> pdb=" O ARG L 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 130 through 134 removed outlier: 5.919A pdb=" N TYR L 186 " --> pdb=" O ASP L 154 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 160 through 164 904 hydrogen bonds defined for protein. 2283 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.88 Time building geometry restraints manager: 9.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6937 1.34 - 1.46: 5361 1.46 - 1.58: 9572 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 22008 Sorted by residual: bond pdb=" C3 MAN U 4 " pdb=" O3 MAN U 4 " ideal model delta sigma weight residual 1.408 1.450 -0.042 2.00e-02 2.50e+03 4.31e+00 bond pdb=" C3 MAN O 4 " pdb=" O3 MAN O 4 " ideal model delta sigma weight residual 1.408 1.449 -0.041 2.00e-02 2.50e+03 4.30e+00 bond pdb=" C3 MAN R 4 " pdb=" O3 MAN R 4 " ideal model delta sigma weight residual 1.408 1.449 -0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" C5 MAN O 4 " pdb=" O5 MAN O 4 " ideal model delta sigma weight residual 1.418 1.458 -0.040 2.00e-02 2.50e+03 3.99e+00 bond pdb=" C5 MAN R 4 " pdb=" O5 MAN R 4 " ideal model delta sigma weight residual 1.418 1.457 -0.039 2.00e-02 2.50e+03 3.88e+00 ... (remaining 22003 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.25: 602 106.25 - 113.18: 12477 113.18 - 120.11: 6956 120.11 - 127.05: 9565 127.05 - 133.98: 286 Bond angle restraints: 29886 Sorted by residual: angle pdb=" C GLY K 52 " pdb=" N ASN K 53 " pdb=" CA ASN K 53 " ideal model delta sigma weight residual 121.54 128.97 -7.43 1.91e+00 2.74e-01 1.51e+01 angle pdb=" C GLY I 52 " pdb=" N ASN I 53 " pdb=" CA ASN I 53 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" N GLN G 16 " pdb=" CA GLN G 16 " pdb=" C GLN G 16 " ideal model delta sigma weight residual 108.34 112.74 -4.40 1.31e+00 5.83e-01 1.13e+01 angle pdb=" N LYS G 195 " pdb=" CA LYS G 195 " pdb=" C LYS G 195 " ideal model delta sigma weight residual 110.80 117.37 -6.57 2.13e+00 2.20e-01 9.52e+00 angle pdb=" C2 MAN U 4 " pdb=" C3 MAN U 4 " pdb=" O3 MAN U 4 " ideal model delta sigma weight residual 107.58 116.37 -8.79 3.00e+00 1.11e-01 8.59e+00 ... (remaining 29881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.05: 12989 22.05 - 44.09: 672 44.09 - 66.14: 107 66.14 - 88.18: 52 88.18 - 110.23: 25 Dihedral angle restraints: 13845 sinusoidal: 6087 harmonic: 7758 Sorted by residual: dihedral pdb=" CB CYS G 139 " pdb=" SG CYS G 139 " pdb=" SG CYS G 199 " pdb=" CB CYS G 199 " ideal model delta sinusoidal sigma weight residual 93.00 3.77 89.23 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CB CYS I 139 " pdb=" SG CYS I 139 " pdb=" SG CYS I 199 " pdb=" CB CYS I 199 " ideal model delta sinusoidal sigma weight residual 93.00 28.41 64.59 1 1.00e+01 1.00e-02 5.48e+01 dihedral pdb=" CA CYS E 14 " pdb=" CB CYS E 14 " pdb=" SG CYS E 14 " pdb=" SG CYS F 137 " ideal model delta sinusoidal sigma weight residual -73.00 2.36 -75.36 1 2.00e+01 2.50e-03 1.79e+01 ... (remaining 13842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3106 0.081 - 0.161: 376 0.161 - 0.242: 12 0.242 - 0.322: 10 0.322 - 0.403: 3 Chirality restraints: 3507 Sorted by residual: chirality pdb=" C3 MAN O 4 " pdb=" C2 MAN O 4 " pdb=" C4 MAN O 4 " pdb=" O3 MAN O 4 " both_signs ideal model delta sigma weight residual False 2.47 2.07 0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" C3 MAN U 4 " pdb=" C2 MAN U 4 " pdb=" C4 MAN U 4 " pdb=" O3 MAN U 4 " both_signs ideal model delta sigma weight residual False 2.47 2.07 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C3 MAN R 4 " pdb=" C2 MAN R 4 " pdb=" C4 MAN R 4 " pdb=" O3 MAN R 4 " both_signs ideal model delta sigma weight residual False 2.47 2.07 0.40 2.00e-01 2.50e+01 4.01e+00 ... (remaining 3504 not shown) Planarity restraints: 3795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE J 176 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.88e+00 pdb=" N PRO J 177 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO J 177 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO J 177 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE L 176 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO L 177 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO L 177 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 177 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 176 " 0.040 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO H 177 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO H 177 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 177 " 0.033 5.00e-02 4.00e+02 ... (remaining 3792 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 426 2.67 - 3.23: 20104 3.23 - 3.79: 34653 3.79 - 4.34: 48237 4.34 - 4.90: 79448 Nonbonded interactions: 182868 Sorted by model distance: nonbonded pdb=" OE1 GLN G 129 " pdb=" OG SER G 136 " model vdw 2.114 2.440 nonbonded pdb=" O TYR H 54 " pdb=" O6 MAN O 5 " model vdw 2.170 2.440 nonbonded pdb=" O LYS K 150 " pdb=" OG1 THR K 202 " model vdw 2.186 2.440 nonbonded pdb=" O GLY K 24 " pdb=" OG1 THR K 71 " model vdw 2.193 2.440 nonbonded pdb=" OE1 GLU F 120 " pdb=" NH1 ARG F 123 " model vdw 2.196 2.520 ... (remaining 182863 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) selection = (chain 'I' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) selection = (chain 'K' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'T' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.350 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: 6.600 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 63.940 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.240 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:10.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 : 0.006 0.042 22008 Z= 0.364 Angle : 0.742 8.795 29886 Z= 0.376 Chirality : 0.052 0.403 3507 Planarity : 0.005 0.061 3777 Dihedral : 14.710 110.230 8793 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.13 % Allowed : 0.26 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.16), residues: 2670 helix: 2.31 (0.25), residues: 363 sheet: -0.06 (0.17), residues: 810 loop : -1.00 (0.16), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 222 HIS 0.004 0.001 HIS J 109 PHE 0.015 0.002 PHE L 156 TYR 0.018 0.002 TYR I 145 ARG 0.009 0.001 ARG G 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 342 time to evaluate : 2.430 Fit side-chains revert: symmetry clash REVERT: A 33 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8350 (mm-40) REVERT: A 82 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8601 (mm-30) REVERT: A 189 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7597 (tm-30) REVERT: A 219 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8724 (m) REVERT: A 277 CYS cc_start: 0.6400 (p) cc_final: 0.5989 (p) REVERT: B 27 GLN cc_start: 0.7506 (tt0) cc_final: 0.7042 (tp-100) REVERT: C 219 SER cc_start: 0.8990 (OUTLIER) cc_final: 0.8742 (t) REVERT: D 72 GLU cc_start: 0.7989 (pm20) cc_final: 0.7788 (pm20) REVERT: D 139 LYS cc_start: 0.8848 (tttp) cc_final: 0.8628 (tttm) REVERT: E 82 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8532 (mm-30) REVERT: E 189 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7927 (tm-30) REVERT: E 219 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8398 (m) REVERT: F 72 GLU cc_start: 0.8264 (pm20) cc_final: 0.7965 (pm20) REVERT: F 133 MET cc_start: 0.8484 (mtm) cc_final: 0.7925 (mtp) REVERT: G 55 ASN cc_start: 0.7938 (t0) cc_final: 0.7705 (t0) REVERT: G 63 ARG cc_start: 0.7178 (mtm-85) cc_final: 0.6853 (mtm110) REVERT: G 174 LYS cc_start: 0.7064 (pttm) cc_final: 0.6387 (mtmm) REVERT: H 82 GLU cc_start: 0.8275 (tt0) cc_final: 0.8061 (tt0) REVERT: H 155 TYR cc_start: 0.7662 (p90) cc_final: 0.7443 (p90) REVERT: I 55 ASN cc_start: 0.8219 (t0) cc_final: 0.7961 (t0) REVERT: I 154 LYS cc_start: 0.6265 (tmtt) cc_final: 0.6029 (tptm) REVERT: J 3 GLN cc_start: 0.8360 (tt0) cc_final: 0.8130 (tt0) REVERT: J 212 PRO cc_start: 0.8648 (Cg_exo) cc_final: 0.8411 (Cg_endo) REVERT: K 63 ARG cc_start: 0.6676 (ptt-90) cc_final: 0.6447 (ptt-90) REVERT: L 87 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.7250 (mtt90) outliers start: 3 outliers final: 0 residues processed: 345 average time/residue: 1.4364 time to fit residues: 555.9330 Evaluate side-chains 248 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 245 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain E residue 219 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 242 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 211 GLN B 34 GLN B 125 GLN B 168 ASN B 172 GLN D 125 GLN F 34 GLN F 65 GLN F 78 GLN F 172 GLN G 36 HIS H 43 GLN H 181 GLN I 36 HIS ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 181 GLN K 36 HIS ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22008 Z= 0.361 Angle : 0.683 10.082 29886 Z= 0.338 Chirality : 0.050 0.357 3507 Planarity : 0.005 0.051 3777 Dihedral : 10.583 81.838 3984 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.58 % Allowed : 9.33 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.16), residues: 2670 helix: 2.53 (0.26), residues: 366 sheet: -0.21 (0.17), residues: 855 loop : -0.94 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 222 HIS 0.008 0.002 HIS C 18 PHE 0.015 0.002 PHE F 9 TYR 0.014 0.002 TYR D 157 ARG 0.006 0.001 ARG E 321 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 274 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8641 (mm-30) REVERT: A 189 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7667 (tm-30) REVERT: A 219 SER cc_start: 0.9063 (OUTLIER) cc_final: 0.8835 (m) REVERT: B 27 GLN cc_start: 0.7548 (tt0) cc_final: 0.7102 (tp-100) REVERT: B 38 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8378 (mm) REVERT: B 150 GLU cc_start: 0.7437 (pp20) cc_final: 0.7161 (tm-30) REVERT: C 31 ASP cc_start: 0.8268 (m-30) cc_final: 0.7976 (m-30) REVERT: C 217 ILE cc_start: 0.8564 (mp) cc_final: 0.8355 (mp) REVERT: D 72 GLU cc_start: 0.7952 (pm20) cc_final: 0.7683 (pm20) REVERT: D 74 GLU cc_start: 0.7502 (mp0) cc_final: 0.6992 (mp0) REVERT: D 78 GLN cc_start: 0.8821 (tt0) cc_final: 0.8103 (tt0) REVERT: D 81 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: E 189 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7916 (tm-30) REVERT: E 219 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8588 (m) REVERT: G 55 ASN cc_start: 0.7904 (t0) cc_final: 0.7673 (t0) REVERT: G 63 ARG cc_start: 0.7150 (mtm-85) cc_final: 0.6866 (mtm110) REVERT: G 154 LYS cc_start: 0.6459 (OUTLIER) cc_final: 0.5695 (mttt) REVERT: G 174 LYS cc_start: 0.6878 (pttm) cc_final: 0.6494 (mtmm) REVERT: H 83 MET cc_start: 0.8490 (tpp) cc_final: 0.8211 (mmt) REVERT: H 186 TYR cc_start: 0.7344 (m-80) cc_final: 0.7125 (m-80) REVERT: I 20 ILE cc_start: 0.8973 (mt) cc_final: 0.8694 (mp) REVERT: I 107 LYS cc_start: 0.8043 (tptp) cc_final: 0.7799 (tppt) REVERT: I 167 SER cc_start: 0.8301 (t) cc_final: 0.8095 (m) REVERT: J 82 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8035 (tt0) REVERT: J 212 PRO cc_start: 0.8665 (Cg_exo) cc_final: 0.8434 (Cg_endo) REVERT: K 63 ARG cc_start: 0.6664 (ptt-90) cc_final: 0.6199 (ptt-90) REVERT: K 81 GLN cc_start: 0.6981 (mt0) cc_final: 0.6594 (mp10) REVERT: L 43 GLN cc_start: 0.7430 (mp10) cc_final: 0.7211 (mp-120) outliers start: 37 outliers final: 15 residues processed: 291 average time/residue: 1.5184 time to fit residues: 494.7335 Evaluate side-chains 259 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 238 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 154 LYS Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 134 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 201 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 262 optimal weight: 0.9980 chunk 216 optimal weight: 1.9990 chunk 240 optimal weight: 20.0000 chunk 82 optimal weight: 0.2980 chunk 194 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN B 34 GLN B 78 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN C 210 GLN D 125 GLN F 34 GLN F 60 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 GLN ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 181 GLN ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22008 Z= 0.285 Angle : 0.633 9.747 29886 Z= 0.312 Chirality : 0.049 0.340 3507 Planarity : 0.004 0.047 3777 Dihedral : 10.141 76.482 3983 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.23 % Allowed : 11.55 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2670 helix: 2.50 (0.25), residues: 366 sheet: -0.16 (0.17), residues: 861 loop : -0.96 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 47 HIS 0.009 0.001 HIS G 36 PHE 0.013 0.002 PHE F 9 TYR 0.012 0.002 TYR D 162 ARG 0.006 0.000 ARG C 321 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 257 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8626 (mm-30) REVERT: A 189 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7561 (tm-30) REVERT: B 27 GLN cc_start: 0.7552 (tt0) cc_final: 0.7091 (tp-100) REVERT: B 38 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8387 (mm) REVERT: B 150 GLU cc_start: 0.7533 (pp20) cc_final: 0.7270 (tm-30) REVERT: C 31 ASP cc_start: 0.8106 (m-30) cc_final: 0.7863 (m-30) REVERT: D 11 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7853 (pp20) REVERT: D 53 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7554 (m110) REVERT: D 72 GLU cc_start: 0.7935 (pm20) cc_final: 0.7675 (pm20) REVERT: D 74 GLU cc_start: 0.7462 (mp0) cc_final: 0.7185 (mp0) REVERT: D 81 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7903 (mt-10) REVERT: E 189 GLN cc_start: 0.8086 (tm-30) cc_final: 0.7849 (tm-30) REVERT: E 219 SER cc_start: 0.8802 (OUTLIER) cc_final: 0.8493 (m) REVERT: G 55 ASN cc_start: 0.7837 (t0) cc_final: 0.7605 (t0) REVERT: G 63 ARG cc_start: 0.7068 (mtm-85) cc_final: 0.6778 (mtm110) REVERT: G 87 ASP cc_start: 0.7967 (t0) cc_final: 0.7634 (t0) REVERT: G 154 LYS cc_start: 0.6501 (OUTLIER) cc_final: 0.5812 (mttt) REVERT: G 174 LYS cc_start: 0.6881 (pttm) cc_final: 0.6475 (mtmm) REVERT: H 82 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: H 181 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7365 (mt0) REVERT: I 20 ILE cc_start: 0.8976 (mt) cc_final: 0.8675 (mp) REVERT: I 107 LYS cc_start: 0.7971 (tptp) cc_final: 0.7745 (tppt) REVERT: J 212 PRO cc_start: 0.8663 (Cg_exo) cc_final: 0.8436 (Cg_endo) REVERT: K 63 ARG cc_start: 0.6781 (ptt-90) cc_final: 0.6364 (ptt-90) REVERT: K 81 GLN cc_start: 0.6993 (mt0) cc_final: 0.6581 (mp10) REVERT: L 62 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8477 (tmtt) outliers start: 52 outliers final: 28 residues processed: 282 average time/residue: 1.4541 time to fit residues: 461.8620 Evaluate side-chains 276 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 239 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 154 LYS Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 239 optimal weight: 0.6980 chunk 182 optimal weight: 0.1980 chunk 126 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 243 optimal weight: 8.9990 chunk 258 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 231 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN B 34 GLN B 172 GLN D 125 GLN F 34 GLN F 60 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN G 36 HIS H 43 GLN H 181 GLN I 36 HIS ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 181 GLN ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN L 181 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 22008 Z= 0.267 Angle : 0.628 11.547 29886 Z= 0.308 Chirality : 0.049 0.374 3507 Planarity : 0.004 0.047 3777 Dihedral : 9.579 70.458 3982 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.52 % Allowed : 12.92 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.16), residues: 2670 helix: 2.54 (0.26), residues: 366 sheet: -0.14 (0.17), residues: 858 loop : -0.93 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 47 HIS 0.005 0.001 HIS D 64 PHE 0.013 0.002 PHE F 9 TYR 0.013 0.001 TYR D 162 ARG 0.007 0.000 ARG C 321 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 263 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8621 (mm-30) REVERT: A 189 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7563 (tm-30) REVERT: B 27 GLN cc_start: 0.7572 (tt0) cc_final: 0.7163 (tp-100) REVERT: B 38 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8371 (mm) REVERT: B 150 GLU cc_start: 0.7544 (pp20) cc_final: 0.7281 (tm-30) REVERT: C 31 ASP cc_start: 0.8106 (m-30) cc_final: 0.7866 (m-30) REVERT: C 33 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8656 (mm-40) REVERT: C 195 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.6645 (m-80) REVERT: C 321 ARG cc_start: 0.8659 (ttt90) cc_final: 0.8373 (ttt-90) REVERT: D 53 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7528 (m110) REVERT: D 72 GLU cc_start: 0.7950 (pm20) cc_final: 0.7667 (pm20) REVERT: D 74 GLU cc_start: 0.7419 (mp0) cc_final: 0.7189 (mp0) REVERT: D 81 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7936 (mt-10) REVERT: E 190 GLU cc_start: 0.8664 (tt0) cc_final: 0.8436 (tt0) REVERT: F 27 GLN cc_start: 0.7653 (tp40) cc_final: 0.7232 (tm-30) REVERT: G 55 ASN cc_start: 0.7724 (t0) cc_final: 0.7503 (t0) REVERT: G 63 ARG cc_start: 0.7133 (mtm-85) cc_final: 0.6728 (mtm110) REVERT: G 87 ASP cc_start: 0.7973 (t0) cc_final: 0.7651 (t0) REVERT: G 154 LYS cc_start: 0.6502 (OUTLIER) cc_final: 0.5817 (mttt) REVERT: G 174 LYS cc_start: 0.6806 (pttm) cc_final: 0.6455 (mtmm) REVERT: H 82 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: H 186 TYR cc_start: 0.7151 (m-80) cc_final: 0.6902 (m-80) REVERT: I 20 ILE cc_start: 0.8959 (mt) cc_final: 0.8687 (mp) REVERT: I 107 LYS cc_start: 0.7945 (tptp) cc_final: 0.7737 (tppt) REVERT: J 82 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8002 (tt0) REVERT: K 63 ARG cc_start: 0.6926 (ptt-90) cc_final: 0.6472 (ptt-90) REVERT: K 81 GLN cc_start: 0.7015 (mt0) cc_final: 0.6626 (mp10) REVERT: L 62 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8479 (tmtt) outliers start: 59 outliers final: 30 residues processed: 297 average time/residue: 1.4165 time to fit residues: 475.2681 Evaluate side-chains 272 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 234 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 154 LYS Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 214 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 192 optimal weight: 0.7980 chunk 106 optimal weight: 0.3980 chunk 220 optimal weight: 9.9990 chunk 178 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 231 optimal weight: 0.0980 chunk 65 optimal weight: 0.0770 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN B 34 GLN B 78 GLN B 172 GLN D 125 GLN D 168 ASN E 17 HIS F 34 GLN F 60 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN G 36 HIS G 40 GLN H 39 GLN H 181 GLN I 36 HIS ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 181 GLN ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22008 Z= 0.168 Angle : 0.610 16.174 29886 Z= 0.298 Chirality : 0.048 0.339 3507 Planarity : 0.004 0.046 3777 Dihedral : 9.009 64.771 3981 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.27 % Allowed : 13.91 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.16), residues: 2670 helix: 2.71 (0.26), residues: 366 sheet: -0.26 (0.17), residues: 921 loop : -0.74 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 47 HIS 0.004 0.001 HIS G 36 PHE 0.013 0.001 PHE F 9 TYR 0.014 0.001 TYR B 162 ARG 0.006 0.000 ARG C 321 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 255 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8463 (mm-40) REVERT: A 82 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8618 (mm-30) REVERT: A 189 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7585 (tm-30) REVERT: B 27 GLN cc_start: 0.7518 (tt0) cc_final: 0.7133 (tp-100) REVERT: B 150 GLU cc_start: 0.7675 (pp20) cc_final: 0.7282 (tm-30) REVERT: C 31 ASP cc_start: 0.8087 (m-30) cc_final: 0.7839 (m-30) REVERT: C 195 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.6645 (m-80) REVERT: D 11 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7871 (pp20) REVERT: D 53 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7468 (m110) REVERT: D 72 GLU cc_start: 0.7941 (pm20) cc_final: 0.7675 (pm20) REVERT: D 74 GLU cc_start: 0.7415 (mp0) cc_final: 0.6937 (mp0) REVERT: D 78 GLN cc_start: 0.8835 (tt0) cc_final: 0.8288 (tt0) REVERT: D 85 GLU cc_start: 0.8267 (tp30) cc_final: 0.8051 (tp30) REVERT: D 139 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8510 (tttp) REVERT: F 27 GLN cc_start: 0.7588 (tp40) cc_final: 0.7080 (tm-30) REVERT: F 81 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8205 (mt-10) REVERT: G 63 ARG cc_start: 0.7161 (mtm-85) cc_final: 0.6880 (mtm110) REVERT: G 87 ASP cc_start: 0.7914 (t0) cc_final: 0.7623 (t0) REVERT: G 154 LYS cc_start: 0.6393 (mmpt) cc_final: 0.5695 (mtmt) REVERT: G 174 LYS cc_start: 0.6805 (pttm) cc_final: 0.6445 (mtmm) REVERT: I 20 ILE cc_start: 0.8922 (mt) cc_final: 0.8641 (mp) REVERT: J 179 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8440 (p) REVERT: K 63 ARG cc_start: 0.6817 (ptt-90) cc_final: 0.6487 (ptt-90) REVERT: K 81 GLN cc_start: 0.6979 (mt0) cc_final: 0.6732 (mm-40) REVERT: L 62 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8352 (tmtt) outliers start: 53 outliers final: 27 residues processed: 288 average time/residue: 1.4501 time to fit residues: 474.8994 Evaluate side-chains 273 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 239 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 0.5980 chunk 232 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 151 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 258 optimal weight: 0.1980 chunk 214 optimal weight: 3.9990 chunk 119 optimal weight: 0.0070 chunk 21 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN B 34 GLN B 60 ASN B 172 GLN F 34 GLN F 60 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN G 36 HIS H 181 GLN ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 181 GLN ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22008 Z= 0.171 Angle : 0.602 14.395 29886 Z= 0.292 Chirality : 0.047 0.339 3507 Planarity : 0.004 0.046 3777 Dihedral : 8.582 60.443 3981 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.23 % Allowed : 14.72 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 2670 helix: 2.80 (0.26), residues: 366 sheet: -0.19 (0.17), residues: 921 loop : -0.72 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 47 HIS 0.004 0.001 HIS G 36 PHE 0.013 0.001 PHE F 9 TYR 0.014 0.001 TYR D 162 ARG 0.008 0.000 ARG C 321 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 254 time to evaluate : 2.377 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: A 33 GLN cc_start: 0.8940 (mm-40) cc_final: 0.8484 (mm-40) REVERT: A 82 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8613 (mm-30) REVERT: A 189 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7674 (tm-30) REVERT: B 27 GLN cc_start: 0.7525 (tt0) cc_final: 0.7228 (tp-100) REVERT: B 150 GLU cc_start: 0.7595 (pp20) cc_final: 0.7192 (tm-30) REVERT: C 31 ASP cc_start: 0.8159 (m-30) cc_final: 0.7926 (m-30) REVERT: C 195 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.6626 (m-80) REVERT: D 11 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7866 (pp20) REVERT: D 72 GLU cc_start: 0.7938 (pm20) cc_final: 0.7670 (pm20) REVERT: D 74 GLU cc_start: 0.7411 (mp0) cc_final: 0.7034 (mp0) REVERT: D 78 GLN cc_start: 0.8828 (tt0) cc_final: 0.8276 (tt0) REVERT: F 27 GLN cc_start: 0.7666 (tp40) cc_final: 0.7166 (tm-30) REVERT: F 74 GLU cc_start: 0.7720 (mp0) cc_final: 0.7151 (mp0) REVERT: F 81 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8205 (mt-10) REVERT: G 63 ARG cc_start: 0.7174 (mtm-85) cc_final: 0.6962 (mtm110) REVERT: G 87 ASP cc_start: 0.7894 (t0) cc_final: 0.7643 (t0) REVERT: G 154 LYS cc_start: 0.6378 (OUTLIER) cc_final: 0.5720 (mtmt) REVERT: G 174 LYS cc_start: 0.6802 (pttm) cc_final: 0.6442 (mtmm) REVERT: H 81 MET cc_start: 0.9003 (ttp) cc_final: 0.8560 (tmm) REVERT: I 20 ILE cc_start: 0.8896 (mt) cc_final: 0.8620 (mp) REVERT: J 129 PRO cc_start: 0.8667 (Cg_endo) cc_final: 0.8277 (Cg_exo) REVERT: J 179 VAL cc_start: 0.8701 (OUTLIER) cc_final: 0.8429 (p) REVERT: K 81 GLN cc_start: 0.6986 (mt0) cc_final: 0.6741 (mm-40) REVERT: L 62 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8325 (tmtt) REVERT: L 65 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8232 (mm110) outliers start: 52 outliers final: 27 residues processed: 289 average time/residue: 1.4336 time to fit residues: 466.8463 Evaluate side-chains 273 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 240 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain G residue 36 HIS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 154 LYS Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 249 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 257 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN B 34 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN D 47 GLN D 60 ASN D 78 GLN ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN F 60 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN H 43 GLN H 181 GLN ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 181 GLN ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 22008 Z= 0.435 Angle : 0.698 15.013 29886 Z= 0.343 Chirality : 0.051 0.327 3507 Planarity : 0.005 0.051 3777 Dihedral : 8.838 62.165 3981 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.87 % Allowed : 14.93 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.16), residues: 2670 helix: 2.50 (0.26), residues: 366 sheet: -0.23 (0.17), residues: 903 loop : -0.84 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 37 HIS 0.014 0.002 HIS G 36 PHE 0.016 0.002 PHE F 9 TYR 0.015 0.002 TYR E 195 ARG 0.006 0.001 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 229 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8716 (tp) REVERT: A 82 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8628 (mm-30) REVERT: A 189 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7598 (tm-30) REVERT: A 195 TYR cc_start: 0.8661 (OUTLIER) cc_final: 0.6625 (m-80) REVERT: B 27 GLN cc_start: 0.7577 (tt0) cc_final: 0.7207 (tp-100) REVERT: B 38 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8408 (mm) REVERT: B 150 GLU cc_start: 0.7471 (pp20) cc_final: 0.7173 (tm-30) REVERT: C 31 ASP cc_start: 0.8139 (m-30) cc_final: 0.7908 (m-30) REVERT: C 195 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.6832 (m-80) REVERT: C 209 SER cc_start: 0.8761 (p) cc_final: 0.8556 (m) REVERT: C 219 SER cc_start: 0.9005 (OUTLIER) cc_final: 0.8755 (m) REVERT: D 53 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7578 (m110) REVERT: D 60 ASN cc_start: 0.7896 (m-40) cc_final: 0.7454 (m-40) REVERT: D 72 GLU cc_start: 0.8020 (pm20) cc_final: 0.7732 (pm20) REVERT: D 150 GLU cc_start: 0.7633 (pp20) cc_final: 0.7078 (tm-30) REVERT: F 27 GLN cc_start: 0.7687 (tp40) cc_final: 0.7170 (tm-30) REVERT: F 74 GLU cc_start: 0.7728 (mp0) cc_final: 0.7352 (mp0) REVERT: F 81 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8223 (mt-10) REVERT: G 63 ARG cc_start: 0.7281 (mtm-85) cc_final: 0.6887 (mtm110) REVERT: G 87 ASP cc_start: 0.8039 (t0) cc_final: 0.7741 (t0) REVERT: G 154 LYS cc_start: 0.6420 (OUTLIER) cc_final: 0.5762 (mtmt) REVERT: G 174 LYS cc_start: 0.6620 (pttm) cc_final: 0.6259 (mtmm) REVERT: G 184 LEU cc_start: 0.7195 (pt) cc_final: 0.6837 (tp) REVERT: H 181 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7085 (mp10) REVERT: I 20 ILE cc_start: 0.8950 (mt) cc_final: 0.8683 (mp) REVERT: J 82 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8058 (tt0) REVERT: K 81 GLN cc_start: 0.7039 (mt0) cc_final: 0.6602 (mp10) REVERT: L 62 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8495 (tmtt) outliers start: 67 outliers final: 39 residues processed: 275 average time/residue: 1.4192 time to fit residues: 440.7991 Evaluate side-chains 272 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 222 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 154 LYS Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 159 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 175 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN B 34 GLN B 172 GLN F 34 GLN F 60 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN H 181 GLN ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 181 GLN ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22008 Z= 0.285 Angle : 0.646 13.538 29886 Z= 0.317 Chirality : 0.049 0.330 3507 Planarity : 0.004 0.047 3777 Dihedral : 8.578 59.974 3981 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.70 % Allowed : 15.40 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.16), residues: 2670 helix: 2.53 (0.26), residues: 366 sheet: -0.26 (0.17), residues: 921 loop : -0.78 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 47 HIS 0.004 0.001 HIS D 64 PHE 0.016 0.002 PHE F 9 TYR 0.015 0.001 TYR D 162 ARG 0.010 0.000 ARG E 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 236 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8712 (tp) REVERT: A 82 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8602 (mm-30) REVERT: A 189 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7567 (tm-30) REVERT: A 195 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.6612 (m-80) REVERT: B 27 GLN cc_start: 0.7538 (tt0) cc_final: 0.7193 (tp-100) REVERT: B 38 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8424 (mm) REVERT: B 150 GLU cc_start: 0.7465 (pp20) cc_final: 0.7173 (tm-30) REVERT: C 31 ASP cc_start: 0.8186 (m-30) cc_final: 0.7957 (m-30) REVERT: C 33 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8624 (mm-40) REVERT: C 195 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.6773 (m-80) REVERT: D 60 ASN cc_start: 0.7881 (m-40) cc_final: 0.7433 (m-40) REVERT: D 72 GLU cc_start: 0.8081 (pm20) cc_final: 0.7663 (pm20) REVERT: F 27 GLN cc_start: 0.7661 (tp40) cc_final: 0.7163 (tm-30) REVERT: F 74 GLU cc_start: 0.7681 (mp0) cc_final: 0.7329 (mp0) REVERT: F 81 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8196 (mt-10) REVERT: G 63 ARG cc_start: 0.7305 (mtm-85) cc_final: 0.6980 (mtm110) REVERT: G 87 ASP cc_start: 0.7992 (t0) cc_final: 0.7662 (t0) REVERT: G 154 LYS cc_start: 0.6404 (OUTLIER) cc_final: 0.5715 (mtmt) REVERT: G 174 LYS cc_start: 0.6479 (pttm) cc_final: 0.6167 (mtmm) REVERT: G 184 LEU cc_start: 0.7184 (pt) cc_final: 0.6832 (tp) REVERT: H 181 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7489 (mp10) REVERT: I 20 ILE cc_start: 0.8941 (mt) cc_final: 0.8694 (mp) REVERT: J 129 PRO cc_start: 0.8655 (Cg_endo) cc_final: 0.8251 (Cg_exo) REVERT: K 81 GLN cc_start: 0.7017 (mt0) cc_final: 0.6717 (mm-40) REVERT: L 62 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8494 (tmtt) outliers start: 63 outliers final: 38 residues processed: 281 average time/residue: 1.3679 time to fit residues: 435.2076 Evaluate side-chains 270 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 224 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 154 LYS Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 234 optimal weight: 0.3980 chunk 246 optimal weight: 0.5980 chunk 224 optimal weight: 8.9990 chunk 239 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 216 optimal weight: 0.1980 chunk 226 optimal weight: 0.9980 chunk 238 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN B 34 GLN B 172 GLN F 60 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN H 43 GLN H 181 GLN I 36 HIS I 91 GLN ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 181 GLN ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 HIS L 181 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22008 Z= 0.208 Angle : 0.617 12.041 29886 Z= 0.302 Chirality : 0.048 0.335 3507 Planarity : 0.004 0.046 3777 Dihedral : 8.147 56.992 3981 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.31 % Allowed : 16.00 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.16), residues: 2670 helix: 2.62 (0.26), residues: 366 sheet: -0.22 (0.17), residues: 921 loop : -0.74 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 50 HIS 0.004 0.001 HIS G 203 PHE 0.022 0.001 PHE G 144 TYR 0.017 0.001 TYR B 162 ARG 0.011 0.000 ARG E 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 236 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8606 (mm-30) REVERT: A 189 GLN cc_start: 0.7845 (tm-30) cc_final: 0.7592 (tm-30) REVERT: A 195 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.6545 (m-80) REVERT: B 27 GLN cc_start: 0.7508 (tt0) cc_final: 0.7177 (tp-100) REVERT: B 38 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8419 (mm) REVERT: B 60 ASN cc_start: 0.7810 (m-40) cc_final: 0.7566 (t0) REVERT: B 150 GLU cc_start: 0.7540 (pp20) cc_final: 0.7186 (tm-30) REVERT: C 31 ASP cc_start: 0.8176 (m-30) cc_final: 0.7937 (m-30) REVERT: C 195 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.6683 (m-80) REVERT: D 60 ASN cc_start: 0.7878 (m-40) cc_final: 0.7440 (m-40) REVERT: D 72 GLU cc_start: 0.8070 (pm20) cc_final: 0.7656 (pm20) REVERT: F 27 GLN cc_start: 0.7634 (tp40) cc_final: 0.7178 (tm-30) REVERT: F 81 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8212 (mt-10) REVERT: G 63 ARG cc_start: 0.7260 (mtm-85) cc_final: 0.6909 (mtm110) REVERT: G 81 GLN cc_start: 0.7365 (pm20) cc_final: 0.6671 (pm20) REVERT: G 87 ASP cc_start: 0.7949 (t0) cc_final: 0.7650 (t0) REVERT: G 154 LYS cc_start: 0.6533 (OUTLIER) cc_final: 0.5890 (mtmt) REVERT: G 184 LEU cc_start: 0.7149 (pt) cc_final: 0.6821 (tp) REVERT: H 181 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7507 (mp10) REVERT: I 20 ILE cc_start: 0.8922 (mt) cc_final: 0.8668 (mp) REVERT: J 129 PRO cc_start: 0.8637 (Cg_endo) cc_final: 0.8253 (Cg_exo) REVERT: K 81 GLN cc_start: 0.7005 (mt0) cc_final: 0.6685 (mm-40) REVERT: L 62 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8505 (tmtt) outliers start: 54 outliers final: 35 residues processed: 273 average time/residue: 1.4055 time to fit residues: 433.0052 Evaluate side-chains 269 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 227 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 154 LYS Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 157 optimal weight: 9.9990 chunk 253 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 266 optimal weight: 0.0670 chunk 244 optimal weight: 6.9990 chunk 211 optimal weight: 0.7980 chunk 21 optimal weight: 0.0060 chunk 163 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.7736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN B 34 GLN B 172 GLN F 34 GLN F 60 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN H 181 GLN I 36 HIS ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 181 GLN ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22008 Z= 0.235 Angle : 0.628 12.807 29886 Z= 0.308 Chirality : 0.048 0.333 3507 Planarity : 0.004 0.046 3777 Dihedral : 7.994 57.914 3981 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.14 % Allowed : 16.17 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 2670 helix: 2.62 (0.26), residues: 366 sheet: -0.20 (0.17), residues: 921 loop : -0.74 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 37 HIS 0.004 0.001 HIS G 203 PHE 0.025 0.001 PHE G 144 TYR 0.019 0.001 TYR B 162 ARG 0.010 0.000 ARG E 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 233 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8604 (mm-30) REVERT: A 189 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7604 (tm-30) REVERT: A 195 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.6546 (m-80) REVERT: B 27 GLN cc_start: 0.7519 (tt0) cc_final: 0.7182 (tp-100) REVERT: B 38 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8423 (mm) REVERT: B 60 ASN cc_start: 0.7816 (m-40) cc_final: 0.7570 (t0) REVERT: B 150 GLU cc_start: 0.7540 (pp20) cc_final: 0.7185 (tm-30) REVERT: C 195 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.6691 (m-80) REVERT: D 11 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7973 (pp20) REVERT: D 53 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7528 (m110) REVERT: D 60 ASN cc_start: 0.7886 (m-40) cc_final: 0.7443 (m-40) REVERT: D 72 GLU cc_start: 0.8054 (pm20) cc_final: 0.7679 (pm20) REVERT: F 27 GLN cc_start: 0.7632 (tp40) cc_final: 0.7146 (tm-30) REVERT: F 81 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8212 (mt-10) REVERT: G 63 ARG cc_start: 0.7264 (mtm-85) cc_final: 0.6904 (mtm110) REVERT: G 81 GLN cc_start: 0.7307 (pm20) cc_final: 0.6593 (pm20) REVERT: G 87 ASP cc_start: 0.7964 (t0) cc_final: 0.7661 (t0) REVERT: G 154 LYS cc_start: 0.6531 (OUTLIER) cc_final: 0.5862 (mtmt) REVERT: G 184 LEU cc_start: 0.7151 (pt) cc_final: 0.6822 (tp) REVERT: H 181 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7660 (mp10) REVERT: I 20 ILE cc_start: 0.8923 (mt) cc_final: 0.8668 (mp) REVERT: J 82 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: J 129 PRO cc_start: 0.8632 (Cg_endo) cc_final: 0.8254 (Cg_exo) REVERT: L 62 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8509 (tmtt) outliers start: 50 outliers final: 35 residues processed: 268 average time/residue: 1.3960 time to fit residues: 424.1962 Evaluate side-chains 268 residues out of total 2334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 223 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 154 LYS Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 181 GLN Chi-restraints excluded: chain I residue 36 HIS Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 168 optimal weight: 0.5980 chunk 225 optimal weight: 0.0570 chunk 64 optimal weight: 0.6980 chunk 195 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN B 34 GLN B 172 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN F 60 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 GLN I 36 HIS ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 181 GLN ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.142971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.100309 restraints weight = 29168.256| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.15 r_work: 0.2814 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22008 Z= 0.254 Angle : 0.642 15.124 29886 Z= 0.314 Chirality : 0.048 0.332 3507 Planarity : 0.004 0.046 3777 Dihedral : 7.898 58.575 3981 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.44 % Allowed : 16.26 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.16), residues: 2670 helix: 2.59 (0.26), residues: 366 sheet: -0.20 (0.17), residues: 921 loop : -0.76 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 37 HIS 0.007 0.001 HIS I 36 PHE 0.024 0.001 PHE G 144 TYR 0.017 0.001 TYR B 162 ARG 0.010 0.000 ARG E 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8308.85 seconds wall clock time: 148 minutes 21.33 seconds (8901.33 seconds total)