Starting phenix.real_space_refine on Mon Mar 18 21:25:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjp_0235/03_2024/6hjp_0235_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjp_0235/03_2024/6hjp_0235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjp_0235/03_2024/6hjp_0235.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjp_0235/03_2024/6hjp_0235.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjp_0235/03_2024/6hjp_0235_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjp_0235/03_2024/6hjp_0235_updated.pdb" } resolution = 3.3 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= 0.002 sd= 0.123 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 90 5.16 5 C 13878 2.51 5 N 3690 2.21 5 O 4476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 106": "NH1" <-> "NH2" Residue "C TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 106": "NH1" <-> "NH2" Residue "E TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 106": "NH1" <-> "NH2" Residue "G PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "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: 22134 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2510 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 17, 'TRANS': 306} Chain: "B" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1403 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain: "C" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2510 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 17, 'TRANS': 306} Chain: "D" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1403 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain: "E" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2510 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 17, 'TRANS': 306} Chain: "F" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1403 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain: "G" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1611 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 204} Chain: "H" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 201} Chain: "I" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1611 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 204} Chain: "K" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1611 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 204} Chain: "J" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 201} Chain: "L" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 201} 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.11, per 1000 atoms: 0.50 Number of scatterers: 22134 At special positions: 0 Unit cell: (178.948, 164.934, 174.636, 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 90 16.00 O 4476 8.00 N 3690 7.00 C 13878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS B 137 " distance=2.04 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.01 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.02 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.04 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS D 137 " distance=2.04 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.01 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.04 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS F 137 " distance=2.05 Simple disulfide: pdb=" SG CYS E 47 " - pdb=" SG CYS E 278 " distance=2.03 Simple disulfide: pdb=" SG CYS E 59 " - pdb=" SG CYS E 71 " distance=2.01 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 306 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.05 Simple disulfide: pdb=" SG CYS G 143 " - pdb=" SG CYS G 199 " distance=2.05 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.05 Simple disulfide: pdb=" SG CYS H 135 " - pdb=" SG CYS H 195 " distance=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.05 Simple disulfide: pdb=" SG CYS I 143 " - pdb=" SG CYS I 199 " distance=2.05 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.05 Simple disulfide: pdb=" SG CYS K 143 " - pdb=" SG CYS K 199 " distance=2.05 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.05 Simple disulfide: pdb=" SG CYS J 135 " - pdb=" SG CYS J 195 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA T 3 " - " MAN T 4 " " BMA Y 3 " - " MAN Y 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA T 3 " - " MAN T 5 " " BMA Y 3 " - " MAN Y 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 S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " BETA1-6 " NAG N 1 " - " FUC N 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 4 " " NAG X 1 " - " FUC X 4 " NAG-ASN " NAG M 1 " - " ASN A 15 " " NAG N 1 " - " ASN A 27 " " NAG O 1 " - " ASN A 91 " " NAG P 1 " - " ASN A 290 " " NAG Q 1 " - " ASN B 154 " " NAG R 1 " - " ASN C 15 " " NAG S 1 " - " ASN C 27 " " NAG T 1 " - " ASN C 91 " " NAG U 1 " - " ASN C 290 " " NAG V 1 " - " ASN D 154 " " NAG W 1 " - " ASN E 15 " " NAG X 1 " - " ASN E 27 " " NAG Y 1 " - " ASN E 91 " " NAG Z 1 " - " ASN E 290 " " NAG a 1 " - " ASN F 154 " Time building additional restraints: 8.47 Conformation dependent library (CDL) restraints added in 3.8 seconds 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 42 sheets defined 15.6% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.40 Creating SS restraints... Processing helix chain 'A' and resid 49 through 50 No H-bonds generated for 'chain 'A' and resid 49 through 50' Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 102 through 111 removed outlier: 3.599A pdb=" N SER A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N SER A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'B' and resid 38 through 58 removed outlier: 3.737A pdb=" N GLN B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 124 removed outlier: 3.954A pdb=" N GLU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 154 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 163 through 173 removed outlier: 3.708A pdb=" N LYS B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 50 No H-bonds generated for 'chain 'C' and resid 49 through 50' Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 102 through 111 removed outlier: 3.598A pdb=" N SER C 110 " --> pdb=" O ARG C 106 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 195 Processing helix chain 'D' and resid 38 through 58 removed outlier: 3.736A pdb=" N GLN D 42 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 124 removed outlier: 3.955A pdb=" N GLU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 154 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 163 through 173 removed outlier: 3.707A pdb=" N LYS D 167 " --> pdb=" O SER D 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 50 No H-bonds generated for 'chain 'E' and resid 49 through 50' Processing helix chain 'E' and resid 61 through 66 Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 102 through 111 removed outlier: 3.598A pdb=" N SER E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N SER E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 195 Processing helix chain 'F' and resid 38 through 58 removed outlier: 3.736A pdb=" N GLN F 42 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 124 removed outlier: 3.954A pdb=" N GLU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 154 Processing helix chain 'F' and resid 159 through 161 No H-bonds generated for 'chain 'F' and resid 159 through 161' Processing helix chain 'F' and resid 163 through 173 removed outlier: 3.707A pdb=" N LYS F 167 " --> pdb=" O SER F 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'H' and resid 123 through 128 Processing helix chain 'H' and resid 184 through 189 Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 88 through 90 No H-bonds generated for 'chain 'I' and resid 88 through 90' Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'J' and resid 123 through 128 Processing helix chain 'J' and resid 184 through 189 Processing helix chain 'L' and resid 123 through 128 Processing helix chain 'L' and resid 184 through 189 Processing sheet with id= A, first strand: chain 'A' and resid 268 through 270 removed outlier: 6.633A pdb=" N ILE A 83 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU A 54 " --> pdb=" O ILE A 84 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.996A pdb=" N MET A 230 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 115 through 118 Processing sheet with id= D, first strand: chain 'A' and resid 164 through 169 Processing sheet with id= E, first strand: chain 'A' and resid 282 through 284 Processing sheet with id= F, first strand: chain 'C' and resid 268 through 270 removed outlier: 6.632A pdb=" N ILE C 83 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU C 54 " --> pdb=" O ILE C 84 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 97 through 99 removed outlier: 6.994A pdb=" N MET C 230 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 115 through 118 Processing sheet with id= I, first strand: chain 'C' and resid 164 through 169 Processing sheet with id= J, first strand: chain 'C' and resid 282 through 284 Processing sheet with id= K, first strand: chain 'E' and resid 268 through 270 removed outlier: 6.633A pdb=" N ILE E 83 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU E 54 " --> pdb=" O ILE E 84 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 97 through 99 removed outlier: 6.995A pdb=" N MET E 230 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 115 through 118 Processing sheet with id= N, first strand: chain 'E' and resid 164 through 169 Processing sheet with id= O, first strand: chain 'E' and resid 282 through 284 Processing sheet with id= P, first strand: chain 'G' and resid 3 through 7 Processing sheet with id= Q, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.868A pdb=" N THR G 119 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ALA G 40 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU G 45 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 129 through 133 removed outlier: 6.149A pdb=" N TYR G 179 " --> pdb=" O ASP G 147 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU G 178 " --> pdb=" O GLN G 174 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 153 through 157 Processing sheet with id= T, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.634A pdb=" N GLU H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER H 67 " --> pdb=" O GLU H 70 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.588A pdb=" N ARG H 104 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL H 13 " --> pdb=" O ARG H 104 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLU H 106 " --> pdb=" O VAL H 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'H' and resid 85 through 90 removed outlier: 3.895A pdb=" N ILE H 48 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLN H 37 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU H 46 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 115 through 119 removed outlier: 5.697A pdb=" N TYR H 174 " --> pdb=" O ASN H 139 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 145 through 151 Processing sheet with id= Y, first strand: chain 'I' and resid 3 through 7 Processing sheet with id= Z, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.863A pdb=" N THR I 119 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA I 40 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU I 45 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 129 through 133 removed outlier: 6.149A pdb=" N TYR I 179 " --> pdb=" O ASP I 147 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU I 178 " --> pdb=" O GLN I 174 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 153 through 157 Processing sheet with id= AC, first strand: chain 'K' and resid 3 through 7 Processing sheet with id= AD, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.865A pdb=" N THR K 119 " --> pdb=" O GLY K 10 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA K 40 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU K 45 " --> pdb=" O ALA K 40 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'K' and resid 129 through 133 removed outlier: 6.149A pdb=" N TYR K 179 " --> pdb=" O ASP K 147 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU K 178 " --> pdb=" O GLN K 174 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 153 through 157 Processing sheet with id= AG, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.634A pdb=" N GLU J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER J 67 " --> pdb=" O GLU J 70 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.588A pdb=" N ARG J 104 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL J 13 " --> pdb=" O ARG J 104 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLU J 106 " --> pdb=" O VAL J 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'J' and resid 85 through 90 removed outlier: 3.895A pdb=" N ILE J 48 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'J' and resid 115 through 119 removed outlier: 5.698A pdb=" N TYR J 174 " --> pdb=" O ASN J 139 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'J' and resid 145 through 151 Processing sheet with id= AL, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.634A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER L 67 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.588A pdb=" N ARG L 104 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL L 13 " --> pdb=" O ARG L 104 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLU L 106 " --> pdb=" O VAL L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'L' and resid 85 through 90 removed outlier: 3.896A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.698A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'L' and resid 145 through 151 678 hydrogen bonds defined for protein. 1863 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.67 Time building geometry restraints manager: 9.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4368 1.32 - 1.45: 5889 1.45 - 1.57: 12246 1.57 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 22623 Sorted by residual: bond pdb=" N GLU B 139 " pdb=" CA GLU B 139 " ideal model delta sigma weight residual 1.459 1.396 0.063 9.10e-03 1.21e+04 4.76e+01 bond pdb=" N GLU F 139 " pdb=" CA GLU F 139 " ideal model delta sigma weight residual 1.459 1.397 0.063 9.10e-03 1.21e+04 4.75e+01 bond pdb=" N GLU D 139 " pdb=" CA GLU D 139 " ideal model delta sigma weight residual 1.459 1.397 0.062 9.10e-03 1.21e+04 4.65e+01 bond pdb=" N HIS D 142 " pdb=" CA HIS D 142 " ideal model delta sigma weight residual 1.456 1.415 0.042 1.14e-02 7.69e+03 1.33e+01 bond pdb=" N HIS F 142 " pdb=" CA HIS F 142 " ideal model delta sigma weight residual 1.456 1.415 0.042 1.14e-02 7.69e+03 1.33e+01 ... (remaining 22618 not shown) Histogram of bond angle deviations from ideal: 97.83 - 105.22: 522 105.22 - 112.61: 11678 112.61 - 120.00: 8195 120.00 - 127.39: 10040 127.39 - 134.78: 288 Bond angle restraints: 30723 Sorted by residual: angle pdb=" CA PHE F 140 " pdb=" CB PHE F 140 " pdb=" CG PHE F 140 " ideal model delta sigma weight residual 113.80 107.03 6.77 1.00e+00 1.00e+00 4.58e+01 angle pdb=" CA PHE D 140 " pdb=" CB PHE D 140 " pdb=" CG PHE D 140 " ideal model delta sigma weight residual 113.80 107.07 6.73 1.00e+00 1.00e+00 4.53e+01 angle pdb=" CA PHE B 140 " pdb=" CB PHE B 140 " pdb=" CG PHE B 140 " ideal model delta sigma weight residual 113.80 107.12 6.68 1.00e+00 1.00e+00 4.47e+01 angle pdb=" C TYR B 141 " pdb=" CA TYR B 141 " pdb=" CB TYR B 141 " ideal model delta sigma weight residual 110.79 101.02 9.77 1.66e+00 3.63e-01 3.46e+01 angle pdb=" C TYR D 141 " pdb=" CA TYR D 141 " pdb=" CB TYR D 141 " ideal model delta sigma weight residual 110.79 101.18 9.61 1.66e+00 3.63e-01 3.35e+01 ... (remaining 30718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.10: 13336 22.10 - 44.21: 578 44.21 - 66.31: 57 66.31 - 88.41: 72 88.41 - 110.52: 36 Dihedral angle restraints: 14079 sinusoidal: 6069 harmonic: 8010 Sorted by residual: dihedral pdb=" C ASP F 158 " pdb=" N ASP F 158 " pdb=" CA ASP F 158 " pdb=" CB ASP F 158 " ideal model delta harmonic sigma weight residual -122.60 -138.20 15.60 0 2.50e+00 1.60e-01 3.90e+01 dihedral pdb=" C ASP B 158 " pdb=" N ASP B 158 " pdb=" CA ASP B 158 " pdb=" CB ASP B 158 " ideal model delta harmonic sigma weight residual -122.60 -137.92 15.32 0 2.50e+00 1.60e-01 3.76e+01 dihedral pdb=" C ASP D 158 " pdb=" N ASP D 158 " pdb=" CA ASP D 158 " pdb=" CB ASP D 158 " ideal model delta harmonic sigma weight residual -122.60 -137.67 15.07 0 2.50e+00 1.60e-01 3.63e+01 ... (remaining 14076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 3411 0.168 - 0.336: 108 0.336 - 0.504: 13 0.504 - 0.672: 2 0.672 - 0.840: 3 Chirality restraints: 3537 Sorted by residual: chirality pdb=" C1 MAN Y 4 " pdb=" O3 BMA Y 3 " pdb=" C2 MAN Y 4 " pdb=" O5 MAN Y 4 " both_signs ideal model delta sigma weight residual False 2.40 1.56 0.84 2.00e-02 2.50e+03 1.77e+03 chirality pdb=" C1 MAN T 4 " pdb=" O3 BMA T 3 " pdb=" C2 MAN T 4 " pdb=" O5 MAN T 4 " both_signs ideal model delta sigma weight residual False 2.40 1.57 0.83 2.00e-02 2.50e+03 1.73e+03 chirality pdb=" C1 MAN O 4 " pdb=" O3 BMA O 3 " pdb=" C2 MAN O 4 " pdb=" O5 MAN O 4 " both_signs ideal model delta sigma weight residual False 2.40 1.59 0.81 2.00e-02 2.50e+03 1.65e+03 ... (remaining 3534 not shown) Planarity restraints: 3915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.339 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" C7 NAG N 1 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.144 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.518 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 1 " -0.339 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" C7 NAG S 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG S 1 " -0.145 2.00e-02 2.50e+03 pdb=" N2 NAG S 1 " 0.517 2.00e-02 2.50e+03 pdb=" O7 NAG S 1 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 1 " -0.338 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG X 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG X 1 " -0.146 2.00e-02 2.50e+03 pdb=" N2 NAG X 1 " 0.516 2.00e-02 2.50e+03 pdb=" O7 NAG X 1 " -0.117 2.00e-02 2.50e+03 ... (remaining 3912 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 981 2.71 - 3.25: 19802 3.25 - 3.80: 33977 3.80 - 4.35: 41605 4.35 - 4.90: 72394 Nonbonded interactions: 168759 Sorted by model distance: nonbonded pdb=" O3 NAG Y 1 " pdb=" O7 NAG Y 1 " model vdw 2.158 2.440 nonbonded pdb=" O3 NAG O 1 " pdb=" O7 NAG O 1 " model vdw 2.159 2.440 nonbonded pdb=" O3 NAG T 1 " pdb=" O7 NAG T 1 " model vdw 2.159 2.440 nonbonded pdb=" OG SER D 151 " pdb=" O THR D 156 " model vdw 2.230 2.440 nonbonded pdb=" OG SER B 151 " pdb=" O THR B 156 " model vdw 2.230 2.440 ... (remaining 168754 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' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'R' selection = chain 'U' selection = chain 'W' selection = chain 'Z' } ncs_group { reference = chain 'N' selection = chain 'S' selection = chain 'X' } ncs_group { reference = chain 'O' selection = chain 'T' selection = chain 'Y' } ncs_group { reference = chain 'Q' selection = chain 'V' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.620 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 30.000 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 56.430 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 22623 Z= 0.523 Angle : 1.170 10.130 30723 Z= 0.697 Chirality : 0.088 0.840 3537 Planarity : 0.018 0.292 3900 Dihedral : 14.764 110.517 8871 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.90 % Favored : 91.88 % Rotamer: Outliers : 2.40 % Allowed : 4.76 % Favored : 92.85 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.14), residues: 2760 helix: -0.78 (0.22), residues: 423 sheet: -0.57 (0.17), residues: 843 loop : -2.46 (0.13), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP E 153 HIS 0.009 0.002 HIS B 25 PHE 0.017 0.003 PHE G 149 TYR 0.023 0.003 TYR B 141 ARG 0.005 0.001 ARG G 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 314 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 211 ARG cc_start: 0.8456 (ttm170) cc_final: 0.8222 (mtp180) REVERT: D 149 MET cc_start: 0.9299 (mmt) cc_final: 0.9027 (mmp) REVERT: F 129 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8303 (p0) REVERT: G 73 ASP cc_start: 0.8348 (t0) cc_final: 0.7743 (t0) REVERT: G 90 ASP cc_start: 0.9123 (m-30) cc_final: 0.8902 (m-30) REVERT: G 174 GLN cc_start: 0.7627 (pt0) cc_final: 0.7407 (pm20) REVERT: G 197 TYR cc_start: 0.6842 (m-80) cc_final: 0.6151 (m-80) REVERT: G 213 ARG cc_start: 0.7851 (ttt180) cc_final: 0.7313 (tmt-80) REVERT: H 4 MET cc_start: 0.8578 (mmm) cc_final: 0.8035 (mmm) REVERT: H 140 PHE cc_start: 0.8139 (p90) cc_final: 0.7696 (p90) REVERT: H 143 ARG cc_start: 0.8918 (tmt-80) cc_final: 0.8332 (tpt90) REVERT: H 166 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8928 (mp0) REVERT: H 168 ASP cc_start: 0.7560 (t70) cc_final: 0.7125 (t0) REVERT: I 6 GLU cc_start: 0.8476 (pt0) cc_final: 0.8205 (pt0) REVERT: I 73 ASP cc_start: 0.8150 (t0) cc_final: 0.7495 (t0) REVERT: I 89 ASP cc_start: 0.9399 (p0) cc_final: 0.9071 (p0) REVERT: I 146 LYS cc_start: 0.8398 (tttp) cc_final: 0.8079 (tptp) REVERT: I 147 ASP cc_start: 0.8601 (m-30) cc_final: 0.8179 (m-30) REVERT: I 211 ASP cc_start: 0.6683 (m-30) cc_final: 0.6185 (t70) REVERT: I 212 LYS cc_start: 0.4815 (tppt) cc_final: 0.4604 (tptt) REVERT: I 215 GLU cc_start: 0.5643 (pt0) cc_final: 0.5416 (tp30) REVERT: K 73 ASP cc_start: 0.8420 (t0) cc_final: 0.7947 (t0) REVERT: K 89 ASP cc_start: 0.9387 (p0) cc_final: 0.9059 (p0) REVERT: K 207 ASN cc_start: 0.8968 (m110) cc_final: 0.8645 (p0) REVERT: J 108 LYS cc_start: 0.9146 (ttpt) cc_final: 0.8702 (tptt) REVERT: J 143 ARG cc_start: 0.8777 (tmt-80) cc_final: 0.8172 (tpt90) REVERT: L 24 ARG cc_start: 0.8539 (mtp-110) cc_final: 0.8265 (mtp-110) REVERT: L 108 LYS cc_start: 0.9034 (ttpt) cc_final: 0.8407 (tptt) REVERT: L 140 PHE cc_start: 0.7780 (p90) cc_final: 0.7495 (p90) REVERT: L 143 ARG cc_start: 0.8676 (tmt-80) cc_final: 0.8417 (tmt-80) outliers start: 57 outliers final: 11 residues processed: 363 average time/residue: 0.4071 time to fit residues: 212.6380 Evaluate side-chains 173 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 129 ASN Chi-restraints excluded: chain G residue 141 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 0.0670 chunk 213 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 247 optimal weight: 10.0000 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 184 HIS A 196 GLN A 239 GLN A 250 ASN A 299 HIS A 323 ASN B 169 ASN C 184 HIS C 250 ASN C 261 ASN C 299 HIS C 323 ASN E 55 GLN E 184 HIS E 239 GLN E 261 ASN E 299 HIS E 323 ASN F 169 ASN G 200 ASN H 6 GLN H 37 GLN H 156 GLN I 13 GLN I 114 GLN K 114 GLN K 200 ASN K 207 ASN J 6 GLN J 37 GLN J 167 GLN L 6 GLN L 37 GLN L 139 ASN L 156 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22623 Z= 0.260 Angle : 0.687 14.028 30723 Z= 0.338 Chirality : 0.046 0.252 3537 Planarity : 0.004 0.056 3900 Dihedral : 12.248 85.401 4006 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.53 % Allowed : 8.63 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: -1.42 (0.15), residues: 2760 helix: 0.87 (0.25), residues: 423 sheet: -0.25 (0.17), residues: 897 loop : -2.03 (0.14), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 255 HIS 0.004 0.001 HIS A 276 PHE 0.019 0.002 PHE I 68 TYR 0.017 0.001 TYR H 193 ARG 0.003 0.001 ARG G 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 174 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8827 (tm-30) REVERT: E 177 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9204 (tp) REVERT: G 73 ASP cc_start: 0.8329 (t0) cc_final: 0.8007 (t0) REVERT: G 90 ASP cc_start: 0.9105 (m-30) cc_final: 0.8870 (m-30) REVERT: G 114 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8561 (tp-100) REVERT: G 197 TYR cc_start: 0.6735 (m-80) cc_final: 0.6045 (m-80) REVERT: G 202 ASN cc_start: 0.7484 (t0) cc_final: 0.7076 (p0) REVERT: G 213 ARG cc_start: 0.7776 (ttt180) cc_final: 0.6937 (tmt-80) REVERT: H 4 MET cc_start: 0.8540 (mmm) cc_final: 0.8123 (mmm) REVERT: H 140 PHE cc_start: 0.7896 (p90) cc_final: 0.7613 (p90) REVERT: H 143 ARG cc_start: 0.8807 (tmt-80) cc_final: 0.8090 (tpt170) REVERT: H 166 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8926 (mp0) REVERT: I 3 GLN cc_start: 0.8282 (pm20) cc_final: 0.8075 (pm20) REVERT: I 73 ASP cc_start: 0.8248 (t0) cc_final: 0.7508 (t0) REVERT: I 76 LYS cc_start: 0.9251 (mtpp) cc_final: 0.8988 (mttm) REVERT: I 89 ASP cc_start: 0.9414 (p0) cc_final: 0.9061 (p0) REVERT: I 146 LYS cc_start: 0.8294 (tttp) cc_final: 0.7896 (tttp) REVERT: I 147 ASP cc_start: 0.8452 (m-30) cc_final: 0.8136 (m-30) REVERT: I 211 ASP cc_start: 0.6581 (m-30) cc_final: 0.6180 (t0) REVERT: I 212 LYS cc_start: 0.4941 (tppt) cc_final: 0.4646 (mmmt) REVERT: I 215 GLU cc_start: 0.5698 (pt0) cc_final: 0.5209 (tp30) REVERT: K 73 ASP cc_start: 0.8447 (t0) cc_final: 0.8072 (t0) REVERT: K 89 ASP cc_start: 0.9364 (p0) cc_final: 0.9065 (p0) REVERT: K 99 MET cc_start: 0.9120 (mmt) cc_final: 0.8824 (mmt) REVERT: J 108 LYS cc_start: 0.9101 (ttpt) cc_final: 0.8612 (tptt) REVERT: J 143 ARG cc_start: 0.8496 (tmt-80) cc_final: 0.8131 (tpt90) REVERT: J 191 LYS cc_start: 0.7170 (ttmp) cc_final: 0.6756 (tmtt) REVERT: L 24 ARG cc_start: 0.8372 (mtp-110) cc_final: 0.7981 (mtp-110) REVERT: L 70 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8462 (mm-30) REVERT: L 106 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: L 108 LYS cc_start: 0.8922 (ttpt) cc_final: 0.8297 (tptt) REVERT: L 143 ARG cc_start: 0.8704 (tmt-80) cc_final: 0.8071 (tpt170) outliers start: 60 outliers final: 32 residues processed: 222 average time/residue: 0.4279 time to fit residues: 137.2913 Evaluate side-chains 181 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 239 GLN Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain H residue 148 GLN Chi-restraints excluded: chain H residue 184 LYS Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain J residue 149 TRP Chi-restraints excluded: chain J residue 168 ASP Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain J residue 211 ASN Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 123 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 206 optimal weight: 0.0470 chunk 168 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 268 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 246 optimal weight: 10.0000 chunk 84 optimal weight: 0.4980 chunk 199 optimal weight: 0.8980 overall best weight: 1.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS C 184 HIS E 184 HIS E 250 ASN E 261 ASN G 114 GLN G 174 GLN K 200 ASN J 167 GLN L 139 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22623 Z= 0.242 Angle : 0.633 16.228 30723 Z= 0.310 Chirality : 0.045 0.184 3537 Planarity : 0.004 0.057 3900 Dihedral : 10.305 79.483 3998 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.44 % Allowed : 9.18 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: -0.90 (0.15), residues: 2760 helix: 1.40 (0.25), residues: 423 sheet: -0.08 (0.17), residues: 921 loop : -1.62 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 255 HIS 0.005 0.001 HIS E 276 PHE 0.023 0.001 PHE L 140 TYR 0.013 0.001 TYR C 102 ARG 0.011 0.000 ARG I 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 149 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 GLN cc_start: 0.9079 (tm-30) cc_final: 0.8828 (tm-30) REVERT: B 98 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9131 (tp) REVERT: G 73 ASP cc_start: 0.8294 (t0) cc_final: 0.7972 (t0) REVERT: G 114 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8589 (tp-100) REVERT: G 197 TYR cc_start: 0.6682 (m-80) cc_final: 0.6048 (m-80) REVERT: G 202 ASN cc_start: 0.7466 (t0) cc_final: 0.6936 (p0) REVERT: G 213 ARG cc_start: 0.7659 (ttt180) cc_final: 0.7147 (tmt-80) REVERT: H 4 MET cc_start: 0.8575 (mmm) cc_final: 0.8151 (mmm) REVERT: H 166 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8891 (mp0) REVERT: I 1 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7832 (tm-30) REVERT: I 73 ASP cc_start: 0.8202 (t0) cc_final: 0.7472 (t0) REVERT: I 76 LYS cc_start: 0.9269 (mtpp) cc_final: 0.9038 (mttm) REVERT: I 89 ASP cc_start: 0.9379 (p0) cc_final: 0.8999 (p0) REVERT: I 146 LYS cc_start: 0.8280 (tttp) cc_final: 0.7886 (tttp) REVERT: I 147 ASP cc_start: 0.8494 (m-30) cc_final: 0.8134 (m-30) REVERT: I 211 ASP cc_start: 0.6621 (m-30) cc_final: 0.6176 (t0) REVERT: I 212 LYS cc_start: 0.4948 (tppt) cc_final: 0.4637 (mmmt) REVERT: I 215 GLU cc_start: 0.5391 (pt0) cc_final: 0.5012 (tp30) REVERT: K 73 ASP cc_start: 0.8318 (t0) cc_final: 0.7944 (t0) REVERT: K 99 MET cc_start: 0.9102 (mmt) cc_final: 0.8785 (mmt) REVERT: K 126 LYS cc_start: 0.8296 (tptp) cc_final: 0.7826 (tmtt) REVERT: J 108 LYS cc_start: 0.9094 (ttpt) cc_final: 0.8617 (tptt) REVERT: J 143 ARG cc_start: 0.8548 (tmt-80) cc_final: 0.8116 (tpt90) REVERT: J 191 LYS cc_start: 0.7171 (ttmp) cc_final: 0.6742 (tmtt) REVERT: L 24 ARG cc_start: 0.8374 (mtp-110) cc_final: 0.7940 (mtp-110) REVERT: L 70 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8385 (mm-30) REVERT: L 106 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7436 (tm-30) REVERT: L 108 LYS cc_start: 0.8914 (ttpt) cc_final: 0.8301 (tptt) REVERT: L 143 ARG cc_start: 0.8639 (tmt-80) cc_final: 0.8161 (tpt170) outliers start: 58 outliers final: 32 residues processed: 198 average time/residue: 0.4039 time to fit residues: 117.9527 Evaluate side-chains 173 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 137 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain H residue 148 GLN Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 190 HIS Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain J residue 168 ASP Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 123 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 128 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 249 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS C 32 HIS C 196 GLN E 261 ASN G 174 GLN I 114 GLN J 167 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 22623 Z= 0.368 Angle : 0.661 18.742 30723 Z= 0.326 Chirality : 0.046 0.185 3537 Planarity : 0.004 0.054 3900 Dihedral : 9.313 72.492 3994 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.07 % Allowed : 9.22 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: -0.67 (0.16), residues: 2760 helix: 1.51 (0.25), residues: 423 sheet: 0.13 (0.17), residues: 912 loop : -1.47 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 149 HIS 0.005 0.001 HIS E 184 PHE 0.023 0.002 PHE H 140 TYR 0.017 0.002 TYR C 102 ARG 0.005 0.001 ARG I 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 140 time to evaluate : 2.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8792 (tm-30) REVERT: B 98 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9140 (tp) REVERT: C 184 HIS cc_start: 0.8512 (OUTLIER) cc_final: 0.7417 (p90) REVERT: E 49 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9070 (mm) REVERT: G 73 ASP cc_start: 0.8162 (t0) cc_final: 0.7898 (t0) REVERT: G 197 TYR cc_start: 0.6748 (m-80) cc_final: 0.6005 (m-80) REVERT: G 202 ASN cc_start: 0.7313 (t0) cc_final: 0.6776 (p0) REVERT: G 213 ARG cc_start: 0.7755 (ttt180) cc_final: 0.7130 (tmt-80) REVERT: H 4 MET cc_start: 0.8656 (mmm) cc_final: 0.8126 (mmm) REVERT: H 166 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8899 (mp0) REVERT: I 73 ASP cc_start: 0.8240 (t0) cc_final: 0.7694 (t0) REVERT: I 146 LYS cc_start: 0.8135 (tttp) cc_final: 0.7727 (tttp) REVERT: I 147 ASP cc_start: 0.8477 (m-30) cc_final: 0.8157 (m-30) REVERT: I 211 ASP cc_start: 0.6682 (m-30) cc_final: 0.6166 (t0) REVERT: I 212 LYS cc_start: 0.5116 (tppt) cc_final: 0.4719 (mmmt) REVERT: I 215 GLU cc_start: 0.5186 (pt0) cc_final: 0.4834 (tp30) REVERT: K 73 ASP cc_start: 0.8284 (t0) cc_final: 0.7898 (t0) REVERT: K 99 MET cc_start: 0.9102 (mmt) cc_final: 0.8778 (mmt) REVERT: K 126 LYS cc_start: 0.8419 (tptp) cc_final: 0.8218 (tptp) REVERT: J 108 LYS cc_start: 0.9033 (ttpt) cc_final: 0.8611 (tptt) REVERT: J 191 LYS cc_start: 0.7156 (ttmp) cc_final: 0.6904 (tptt) REVERT: L 24 ARG cc_start: 0.8404 (mtp-110) cc_final: 0.7995 (mtp-110) REVERT: L 70 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8413 (mm-30) REVERT: L 106 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: L 108 LYS cc_start: 0.8932 (ttpt) cc_final: 0.8308 (tptt) outliers start: 73 outliers final: 44 residues processed: 200 average time/residue: 0.3991 time to fit residues: 117.4854 Evaluate side-chains 183 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 134 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain H residue 148 GLN Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 184 LYS Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain K residue 211 ASP Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 168 ASP Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 123 ASP Chi-restraints excluded: chain L residue 138 ASN Chi-restraints excluded: chain L residue 184 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 236 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 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 231 ASN B 129 ASN D 129 ASN ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 22623 Z= 0.297 Angle : 0.630 20.455 30723 Z= 0.306 Chirality : 0.044 0.227 3537 Planarity : 0.004 0.052 3900 Dihedral : 8.520 62.666 3992 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.90 % Allowed : 10.61 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: -0.47 (0.16), residues: 2760 helix: 1.68 (0.25), residues: 423 sheet: 0.20 (0.17), residues: 924 loop : -1.31 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 149 HIS 0.004 0.001 HIS A 276 PHE 0.021 0.002 PHE H 140 TYR 0.012 0.001 TYR C 102 ARG 0.003 0.000 ARG G 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 142 time to evaluate : 3.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8671 (OUTLIER) cc_final: 0.7645 (p90) REVERT: A 192 GLN cc_start: 0.9079 (tm-30) cc_final: 0.8771 (tm-30) REVERT: B 98 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9133 (tp) REVERT: D 59 MET cc_start: 0.8571 (mmm) cc_final: 0.7830 (mmm) REVERT: E 49 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9046 (mm) REVERT: G 43 LYS cc_start: 0.8726 (mmtp) cc_final: 0.8387 (mmtm) REVERT: G 73 ASP cc_start: 0.8128 (t0) cc_final: 0.7860 (t0) REVERT: G 197 TYR cc_start: 0.6793 (m-80) cc_final: 0.6034 (m-80) REVERT: G 202 ASN cc_start: 0.7292 (t0) cc_final: 0.6716 (p0) REVERT: G 213 ARG cc_start: 0.7766 (ttt180) cc_final: 0.7134 (tmt-80) REVERT: H 4 MET cc_start: 0.8611 (mmm) cc_final: 0.8087 (mmm) REVERT: H 166 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8933 (mp0) REVERT: I 73 ASP cc_start: 0.8257 (t0) cc_final: 0.7737 (t0) REVERT: I 146 LYS cc_start: 0.8147 (tttp) cc_final: 0.7778 (tttp) REVERT: I 147 ASP cc_start: 0.8518 (m-30) cc_final: 0.8145 (m-30) REVERT: I 211 ASP cc_start: 0.6734 (m-30) cc_final: 0.6208 (t0) REVERT: I 212 LYS cc_start: 0.5128 (tppt) cc_final: 0.4729 (mmmt) REVERT: I 215 GLU cc_start: 0.5089 (pt0) cc_final: 0.4783 (tp30) REVERT: K 73 ASP cc_start: 0.8248 (t0) cc_final: 0.7923 (t0) REVERT: K 99 MET cc_start: 0.9088 (mmt) cc_final: 0.8783 (mmt) REVERT: J 108 LYS cc_start: 0.9052 (ttpt) cc_final: 0.8605 (tptt) REVERT: J 109 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7227 (ptm-80) REVERT: J 191 LYS cc_start: 0.7236 (ttmp) cc_final: 0.6979 (tptt) REVERT: L 24 ARG cc_start: 0.8410 (mtp-110) cc_final: 0.7996 (mtp-110) REVERT: L 70 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8418 (mm-30) REVERT: L 106 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: L 108 LYS cc_start: 0.8961 (ttpt) cc_final: 0.8389 (tptt) outliers start: 69 outliers final: 46 residues processed: 199 average time/residue: 0.3933 time to fit residues: 115.7875 Evaluate side-chains 185 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 133 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 129 ASN Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 184 LYS Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain K residue 211 ASP Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 109 ARG Chi-restraints excluded: chain J residue 168 ASP Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 123 ASP Chi-restraints excluded: chain L residue 138 ASN Chi-restraints excluded: chain L residue 187 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 264 optimal weight: 9.9990 chunk 219 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 87 optimal weight: 0.0980 chunk 138 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 129 ASN ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22623 Z= 0.278 Angle : 0.620 21.282 30723 Z= 0.299 Chirality : 0.044 0.237 3537 Planarity : 0.004 0.052 3900 Dihedral : 8.175 57.414 3992 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.07 % Allowed : 10.65 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 2760 helix: 1.78 (0.25), residues: 423 sheet: 0.29 (0.18), residues: 924 loop : -1.22 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 149 HIS 0.004 0.001 HIS A 276 PHE 0.020 0.002 PHE H 140 TYR 0.012 0.001 TYR A 102 ARG 0.004 0.000 ARG J 109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 134 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8721 (OUTLIER) cc_final: 0.7617 (p90) REVERT: A 192 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8775 (tm-30) REVERT: B 98 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9142 (tp) REVERT: C 184 HIS cc_start: 0.8523 (OUTLIER) cc_final: 0.7467 (p90) REVERT: C 296 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: D 59 MET cc_start: 0.8569 (mmm) cc_final: 0.7815 (mmm) REVERT: E 49 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9151 (mt) REVERT: G 43 LYS cc_start: 0.8751 (mmtp) cc_final: 0.8443 (mmtm) REVERT: G 73 ASP cc_start: 0.8120 (t0) cc_final: 0.7774 (t0) REVERT: G 197 TYR cc_start: 0.6784 (m-80) cc_final: 0.6046 (m-80) REVERT: G 213 ARG cc_start: 0.7636 (ttt180) cc_final: 0.6987 (tmt-80) REVERT: H 4 MET cc_start: 0.8645 (mmm) cc_final: 0.8105 (mmm) REVERT: I 73 ASP cc_start: 0.8251 (t0) cc_final: 0.7725 (t0) REVERT: I 146 LYS cc_start: 0.8113 (tttp) cc_final: 0.7728 (tttp) REVERT: I 197 TYR cc_start: 0.7083 (m-80) cc_final: 0.6744 (m-80) REVERT: I 215 GLU cc_start: 0.5090 (pt0) cc_final: 0.4874 (tp30) REVERT: K 73 ASP cc_start: 0.8209 (t0) cc_final: 0.7884 (t0) REVERT: K 99 MET cc_start: 0.9092 (mmt) cc_final: 0.8791 (mmt) REVERT: J 108 LYS cc_start: 0.9064 (ttpt) cc_final: 0.8604 (tptt) REVERT: J 109 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7102 (ptm-80) REVERT: L 24 ARG cc_start: 0.8425 (mtp-110) cc_final: 0.8004 (mtp-110) REVERT: L 70 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8436 (mm-30) REVERT: L 106 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7288 (tm-30) REVERT: L 108 LYS cc_start: 0.8969 (ttpt) cc_final: 0.8399 (tptt) outliers start: 73 outliers final: 52 residues processed: 196 average time/residue: 0.3938 time to fit residues: 116.0265 Evaluate side-chains 192 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 132 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 296 GLN Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 129 ASN Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 184 LYS Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain K residue 211 ASP Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 109 ARG Chi-restraints excluded: chain J residue 168 ASP Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 123 ASP Chi-restraints excluded: chain L residue 138 ASN Chi-restraints excluded: chain L residue 187 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 222 optimal weight: 9.9990 chunk 147 optimal weight: 1.9990 chunk 263 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 ASN C 12 HIS D 129 ASN E 296 GLN ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 GLN L 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 22623 Z= 0.396 Angle : 0.661 22.418 30723 Z= 0.321 Chirality : 0.046 0.230 3537 Planarity : 0.004 0.052 3900 Dihedral : 8.035 56.547 3992 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.95 % Allowed : 11.45 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.16), residues: 2760 helix: 1.73 (0.25), residues: 423 sheet: 0.17 (0.17), residues: 960 loop : -1.25 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP J 149 HIS 0.005 0.002 HIS E 184 PHE 0.021 0.002 PHE E 115 TYR 0.015 0.002 TYR A 102 ARG 0.009 0.001 ARG J 212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 130 time to evaluate : 2.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8811 (OUTLIER) cc_final: 0.7722 (p90) REVERT: A 192 GLN cc_start: 0.9137 (tm-30) cc_final: 0.8835 (tm-30) REVERT: B 98 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9145 (tp) REVERT: C 184 HIS cc_start: 0.8611 (OUTLIER) cc_final: 0.7415 (p90) REVERT: D 59 MET cc_start: 0.8574 (mmm) cc_final: 0.7820 (mmm) REVERT: E 49 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9046 (mm) REVERT: G 43 LYS cc_start: 0.8809 (mmtp) cc_final: 0.8542 (mmtm) REVERT: G 73 ASP cc_start: 0.8156 (t0) cc_final: 0.7862 (t0) REVERT: G 197 TYR cc_start: 0.6823 (m-80) cc_final: 0.6426 (m-80) REVERT: H 4 MET cc_start: 0.8680 (mmm) cc_final: 0.8047 (mmm) REVERT: H 79 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7213 (mp10) REVERT: I 73 ASP cc_start: 0.8271 (t0) cc_final: 0.7752 (t0) REVERT: I 146 LYS cc_start: 0.8113 (tttp) cc_final: 0.7718 (tttp) REVERT: I 147 ASP cc_start: 0.8537 (m-30) cc_final: 0.8158 (m-30) REVERT: I 197 TYR cc_start: 0.7066 (m-80) cc_final: 0.6680 (m-80) REVERT: K 73 ASP cc_start: 0.8189 (t0) cc_final: 0.7839 (t0) REVERT: K 99 MET cc_start: 0.9125 (mmt) cc_final: 0.8819 (mmt) REVERT: J 143 ARG cc_start: 0.8792 (tpt-90) cc_final: 0.8571 (tpt170) REVERT: L 106 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7206 (tm-30) REVERT: L 108 LYS cc_start: 0.8969 (ttpt) cc_final: 0.8405 (tptt) outliers start: 70 outliers final: 52 residues processed: 191 average time/residue: 0.3902 time to fit residues: 112.7454 Evaluate side-chains 184 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 126 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 184 LYS Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain K residue 211 ASP Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 168 ASP Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 123 ASP Chi-restraints excluded: chain L residue 138 ASN Chi-restraints excluded: chain L residue 187 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 206 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 ASN C 231 ASN C 296 GLN D 128 ASN D 129 ASN E 231 ASN E 296 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 GLN L 159 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22623 Z= 0.196 Angle : 0.603 22.364 30723 Z= 0.288 Chirality : 0.043 0.222 3537 Planarity : 0.004 0.050 3900 Dihedral : 7.651 55.838 3992 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.48 % Allowed : 11.83 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 2760 helix: 1.95 (0.25), residues: 423 sheet: 0.32 (0.17), residues: 954 loop : -1.15 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP J 149 HIS 0.004 0.001 HIS A 276 PHE 0.018 0.001 PHE H 140 TYR 0.010 0.001 TYR B 157 ARG 0.007 0.000 ARG J 212 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 132 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8692 (OUTLIER) cc_final: 0.7591 (p90) REVERT: A 192 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8862 (tm-30) REVERT: A 196 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7437 (pt0) REVERT: B 98 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9134 (tp) REVERT: C 184 HIS cc_start: 0.8496 (OUTLIER) cc_final: 0.7441 (p90) REVERT: D 59 MET cc_start: 0.8517 (mmm) cc_final: 0.7837 (mmm) REVERT: G 43 LYS cc_start: 0.8758 (mmtp) cc_final: 0.8453 (mmtm) REVERT: G 73 ASP cc_start: 0.8076 (t0) cc_final: 0.7768 (t0) REVERT: G 197 TYR cc_start: 0.6617 (m-80) cc_final: 0.6276 (m-80) REVERT: H 4 MET cc_start: 0.8645 (mmm) cc_final: 0.8102 (mmm) REVERT: H 79 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.7002 (mp10) REVERT: I 73 ASP cc_start: 0.8234 (t0) cc_final: 0.7570 (t0) REVERT: I 146 LYS cc_start: 0.7971 (tttp) cc_final: 0.7581 (tttp) REVERT: I 197 TYR cc_start: 0.7036 (m-80) cc_final: 0.6680 (m-80) REVERT: K 73 ASP cc_start: 0.8205 (t0) cc_final: 0.7826 (t0) REVERT: K 99 MET cc_start: 0.9097 (mmt) cc_final: 0.8825 (mmt) REVERT: J 108 LYS cc_start: 0.8980 (ttmm) cc_final: 0.8395 (tptt) REVERT: J 143 ARG cc_start: 0.8816 (tpt-90) cc_final: 0.8602 (tpt170) REVERT: L 24 ARG cc_start: 0.8464 (mtp-110) cc_final: 0.8254 (mtp-110) REVERT: L 106 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7212 (tm-30) REVERT: L 108 LYS cc_start: 0.8977 (ttpt) cc_final: 0.8412 (tptt) outliers start: 59 outliers final: 46 residues processed: 182 average time/residue: 0.3901 time to fit residues: 106.5519 Evaluate side-chains 179 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 127 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 184 LYS Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain K residue 211 ASP Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 168 ASP Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 138 ASN Chi-restraints excluded: chain L residue 187 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 6.9990 chunk 252 optimal weight: 6.9990 chunk 229 optimal weight: 0.7980 chunk 245 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 192 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 221 optimal weight: 0.1980 chunk 231 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 261 ASN B 128 ASN B 129 ASN C 183 HIS C 239 GLN C 296 GLN ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 GLN ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 22623 Z= 0.546 Angle : 0.721 24.127 30723 Z= 0.355 Chirality : 0.048 0.201 3537 Planarity : 0.004 0.054 3900 Dihedral : 7.930 58.851 3992 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.78 % Allowed : 11.83 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: -0.37 (0.16), residues: 2760 helix: 1.64 (0.25), residues: 423 sheet: 0.28 (0.18), residues: 915 loop : -1.21 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP J 149 HIS 0.007 0.002 HIS C 12 PHE 0.028 0.002 PHE E 115 TYR 0.016 0.002 TYR A 102 ARG 0.009 0.001 ARG J 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 128 time to evaluate : 2.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8888 (OUTLIER) cc_final: 0.7684 (p90) REVERT: A 192 GLN cc_start: 0.9148 (tm-30) cc_final: 0.8868 (tm-30) REVERT: C 184 HIS cc_start: 0.8775 (OUTLIER) cc_final: 0.7824 (p90) REVERT: G 43 LYS cc_start: 0.8892 (mmtp) cc_final: 0.8623 (mmtm) REVERT: G 73 ASP cc_start: 0.8168 (t0) cc_final: 0.7864 (t0) REVERT: G 197 TYR cc_start: 0.6929 (m-80) cc_final: 0.6516 (m-80) REVERT: H 4 MET cc_start: 0.8773 (mmm) cc_final: 0.7973 (mmm) REVERT: H 79 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7334 (mp10) REVERT: I 43 LYS cc_start: 0.9109 (mmtp) cc_final: 0.8784 (mmtm) REVERT: I 73 ASP cc_start: 0.8283 (t0) cc_final: 0.7599 (t0) REVERT: I 76 LYS cc_start: 0.9285 (mttm) cc_final: 0.9076 (mttm) REVERT: I 146 LYS cc_start: 0.7998 (tttp) cc_final: 0.7595 (tttp) REVERT: I 147 ASP cc_start: 0.8561 (m-30) cc_final: 0.8179 (m-30) REVERT: I 197 TYR cc_start: 0.7104 (m-80) cc_final: 0.6689 (m-80) REVERT: K 73 ASP cc_start: 0.8212 (t0) cc_final: 0.7878 (t0) REVERT: J 143 ARG cc_start: 0.8764 (tpt-90) cc_final: 0.8516 (tpt170) REVERT: L 106 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7178 (tm-30) REVERT: L 108 LYS cc_start: 0.9002 (ttpt) cc_final: 0.8449 (tptt) outliers start: 66 outliers final: 48 residues processed: 186 average time/residue: 0.3909 time to fit residues: 109.3318 Evaluate side-chains 178 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 126 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 184 LYS Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain K residue 211 ASP Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 168 ASP Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 123 ASP Chi-restraints excluded: chain L residue 138 ASN Chi-restraints excluded: chain L residue 187 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 5.9990 chunk 259 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 180 optimal weight: 6.9990 chunk 271 optimal weight: 7.9990 chunk 250 optimal weight: 6.9990 chunk 216 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 167 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN C 239 GLN C 296 GLN ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 GLN ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22623 Z= 0.260 Angle : 0.630 24.291 30723 Z= 0.302 Chirality : 0.044 0.179 3537 Planarity : 0.004 0.078 3900 Dihedral : 7.674 55.849 3992 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.36 % Allowed : 12.29 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: -0.30 (0.16), residues: 2760 helix: 1.83 (0.25), residues: 423 sheet: 0.28 (0.17), residues: 942 loop : -1.21 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP J 149 HIS 0.004 0.001 HIS G 203 PHE 0.017 0.001 PHE H 140 TYR 0.019 0.001 TYR I 80 ARG 0.017 0.001 ARG J 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 132 time to evaluate : 2.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8759 (OUTLIER) cc_final: 0.7654 (p90) REVERT: A 192 GLN cc_start: 0.9111 (tm-30) cc_final: 0.8864 (tm-30) REVERT: C 184 HIS cc_start: 0.8613 (OUTLIER) cc_final: 0.7517 (p90) REVERT: D 59 MET cc_start: 0.8414 (mmm) cc_final: 0.8051 (mmm) REVERT: E 242 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8982 (t) REVERT: F 59 MET cc_start: 0.8442 (mmm) cc_final: 0.8056 (mmm) REVERT: G 43 LYS cc_start: 0.8848 (mmtp) cc_final: 0.8593 (mmtm) REVERT: G 73 ASP cc_start: 0.8168 (t0) cc_final: 0.7778 (t0) REVERT: G 197 TYR cc_start: 0.6780 (m-80) cc_final: 0.6387 (m-80) REVERT: H 4 MET cc_start: 0.8670 (mmm) cc_final: 0.8050 (mmm) REVERT: I 73 ASP cc_start: 0.8246 (t0) cc_final: 0.7693 (t0) REVERT: I 146 LYS cc_start: 0.7978 (tttp) cc_final: 0.7672 (tttp) REVERT: I 197 TYR cc_start: 0.7003 (m-80) cc_final: 0.6574 (m-80) REVERT: K 73 ASP cc_start: 0.8143 (t0) cc_final: 0.7825 (t0) REVERT: K 126 LYS cc_start: 0.8429 (tptp) cc_final: 0.8042 (tmtt) REVERT: L 24 ARG cc_start: 0.8546 (mtp-110) cc_final: 0.8320 (mtp-110) REVERT: L 106 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7161 (tm-30) REVERT: L 108 LYS cc_start: 0.9097 (ttpt) cc_final: 0.8550 (tptt) outliers start: 56 outliers final: 46 residues processed: 179 average time/residue: 0.3987 time to fit residues: 105.7717 Evaluate side-chains 179 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 129 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 184 LYS Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain K residue 211 ASP Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 168 ASP Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 138 ASN Chi-restraints excluded: chain L residue 187 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 0.7980 chunk 230 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 222 optimal weight: 0.0020 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 ASN C 296 GLN D 129 ASN E 296 GLN F 129 ASN ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 GLN I 158 ASN ** I 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN J 167 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.076369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.048644 restraints weight = 63032.031| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 3.43 r_work: 0.2529 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22623 Z= 0.176 Angle : 0.586 23.154 30723 Z= 0.278 Chirality : 0.042 0.183 3537 Planarity : 0.004 0.050 3900 Dihedral : 7.370 59.721 3992 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.19 % Allowed : 12.75 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: -0.00 (0.16), residues: 2760 helix: 2.15 (0.26), residues: 423 sheet: 0.49 (0.18), residues: 927 loop : -1.04 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP J 149 HIS 0.004 0.001 HIS G 203 PHE 0.016 0.001 PHE H 140 TYR 0.009 0.001 TYR B 157 ARG 0.005 0.000 ARG J 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4458.06 seconds wall clock time: 82 minutes 10.42 seconds (4930.42 seconds total)