Starting phenix.real_space_refine on Thu May 1 06:14:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ve8_43168/05_2025/8ve8_43168.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ve8_43168/05_2025/8ve8_43168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ve8_43168/05_2025/8ve8_43168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ve8_43168/05_2025/8ve8_43168.map" model { file = "/net/cci-nas-00/data/ceres_data/8ve8_43168/05_2025/8ve8_43168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ve8_43168/05_2025/8ve8_43168.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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 87 5.16 5 C 6418 2.51 5 N 1682 2.21 5 O 2140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10327 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1520 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "B" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1520 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "C" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1520 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "a" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1243 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain: "b" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1243 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain: "c" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1243 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain: "L" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 530 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'TRANS': 105} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 106 Planarities with less than four sites: {'UNK:plan-1': 106} Unresolved non-hydrogen planarities: 106 Chain: "H" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 595 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'TRANS': 118} Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 119 Planarities with less than four sites: {'UNK:plan-1': 119} Unresolved non-hydrogen planarities: 119 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.10, per 1000 atoms: 0.88 Number of scatterers: 10327 At special positions: 0 Unit cell: (94.058, 101.956, 125.65, 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 87 16.00 O 2140 8.00 N 1682 7.00 C 6418 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=1.29 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.04 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.03 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.08 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=1.63 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.02 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 4 " ALPHA1-6 " BMA N 3 " - " MAN N 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG 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 W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " BETA1-6 " NAG F 1 " - " FUC F 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG J 1 " - " FUC J 3 " " NAG O 1 " - " FUC O 3 " " NAG S 1 " - " FUC S 3 " " NAG X 1 " - " FUC X 3 " NAG-ASN " NAG A 301 " - " ASN A 99 " " NAG A 302 " - " ASN A 119 " " NAG B 301 " - " ASN B 99 " " NAG C 301 " - " ASN C 119 " " NAG C 302 " - " ASN C 99 " " NAG D 1 " - " ASN A 79 " " NAG E 1 " - " ASN A 89 " " NAG F 1 " - " ASN A 109 " " NAG G 1 " - " ASN A 167 " " NAG I 1 " - " ASN A 224 " " NAG J 1 " - " ASN B 109 " " NAG K 1 " - " ASN B 224 " " NAG M 1 " - " ASN B 79 " " NAG N 1 " - " ASN B 89 " " NAG O 1 " - " ASN B 119 " " NAG P 1 " - " ASN B 167 " " NAG Q 1 " - " ASN C 79 " " NAG R 1 " - " ASN C 89 " " NAG S 1 " - " ASN C 109 " " NAG T 1 " - " ASN C 167 " " NAG U 1 " - " ASN C 224 " " NAG V 1 " - " ASN a 365 " " NAG W 1 " - " ASN b 365 " " NAG X 1 " - " ASN b 395 " " NAG Y 1 " - " ASN c 365 " " NAG a 701 " - " ASN a 373 " " NAG a 702 " - " ASN a 390 " " NAG a 703 " - " ASN a 395 " " NAG b 701 " - " ASN b 373 " " NAG b 702 " - " ASN b 390 " " NAG c 701 " - " ASN c 373 " " NAG c 702 " - " ASN c 390 " " NAG c 703 " - " ASN c 395 " Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.0 seconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 18 sheets defined 41.6% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 74 through 81 removed outlier: 3.832A pdb=" N THR A 77 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N MET A 80 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.843A pdb=" N LYS A 161 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.739A pdb=" N ARG A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.663A pdb=" N LEU A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 245 " --> pdb=" O TYR A 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.633A pdb=" N THR B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.532A pdb=" N ALA B 123 " --> pdb=" O ASN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.973A pdb=" N LYS B 161 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.851A pdb=" N GLY B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.894A pdb=" N ILE B 201 " --> pdb=" O GLY B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.827A pdb=" N THR C 77 " --> pdb=" O ASN C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.750A pdb=" N LYS C 161 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.935A pdb=" N ILE C 201 " --> pdb=" O GLY C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 245 Processing helix chain 'C' and resid 246 through 248 No H-bonds generated for 'chain 'C' and resid 246 through 248' Processing helix chain 'a' and resid 294 through 300 removed outlier: 3.899A pdb=" N LYS a 300 " --> pdb=" O THR a 296 " (cutoff:3.500A) Processing helix chain 'a' and resid 301 through 303 No H-bonds generated for 'chain 'a' and resid 301 through 303' Processing helix chain 'a' and resid 307 through 326 removed outlier: 3.505A pdb=" N ASP a 311 " --> pdb=" O GLU a 307 " (cutoff:3.500A) Processing helix chain 'a' and resid 334 through 345 removed outlier: 3.730A pdb=" N LYS a 339 " --> pdb=" O GLN a 335 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ALA a 343 " --> pdb=" O LYS a 339 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.523A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 395 through 398 Processing helix chain 'a' and resid 399 through 413 Processing helix chain 'b' and resid 294 through 299 Processing helix chain 'b' and resid 300 through 303 Processing helix chain 'b' and resid 307 through 326 removed outlier: 3.507A pdb=" N ASP b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) Processing helix chain 'b' and resid 334 through 345 removed outlier: 5.949A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.559A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 399 through 413 Processing helix chain 'c' and resid 281 through 285 removed outlier: 3.520A pdb=" N LEU c 285 " --> pdb=" O ARG c 282 " (cutoff:3.500A) Processing helix chain 'c' and resid 294 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 307 through 326 removed outlier: 3.507A pdb=" N ASP c 311 " --> pdb=" O GLU c 307 " (cutoff:3.500A) Processing helix chain 'c' and resid 334 through 345 removed outlier: 5.994A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU c 344 " --> pdb=" O ALA c 340 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.560A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 399 through 412 removed outlier: 3.943A pdb=" N THR c 412 " --> pdb=" O ASP c 408 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 83 through 86 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 89 removed outlier: 6.805A pdb=" N HIS A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AA4, first strand: chain 'B' and resid 153 through 155 removed outlier: 5.486A pdb=" N THR B 87 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ARG B 235 " --> pdb=" O THR B 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AA6, first strand: chain 'C' and resid 83 through 87 Processing sheet with id=AA7, first strand: chain 'a' and resid 278 through 280 Processing sheet with id=AA8, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AA9, first strand: chain 'b' and resid 278 through 280 Processing sheet with id=AB1, first strand: chain 'b' and resid 388 through 389 Processing sheet with id=AB2, first strand: chain 'c' and resid 278 through 280 Processing sheet with id=AB3, first strand: chain 'c' and resid 388 through 389 Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.286A pdb=" N UNK L 17 " --> pdb=" O UNK L 77 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N UNK L 77 " --> pdb=" O UNK L 17 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AB6, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.575A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N UNK L 49 " --> pdb=" O UNK L 33 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N UNK L 33 " --> pdb=" O UNK L 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 2 through 6 removed outlier: 6.406A pdb=" N UNK H 76 " --> pdb=" O UNK H 72 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 56 through 59 removed outlier: 6.768A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N UNK H 96 " --> pdb=" O UNK H 100D" (cutoff:3.500A) removed outlier: 5.688A pdb=" N UNK H 100D" --> pdb=" O UNK H 96 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 56 through 59 removed outlier: 6.768A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1107 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: 3.45 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 3085 1.34 - 1.47: 2876 1.47 - 1.61: 4412 1.61 - 1.74: 0 1.74 - 1.87: 132 Bond restraints: 10505 Sorted by residual: bond pdb=" N ILE C 213 " pdb=" CA ILE C 213 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.19e-02 7.06e+03 1.38e+01 bond pdb=" C PRO C 83 " pdb=" O PRO C 83 " ideal model delta sigma weight residual 1.233 1.202 0.031 1.10e-02 8.26e+03 7.85e+00 bond pdb=" N CYS C 212 " pdb=" CA CYS C 212 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.10e-02 8.26e+03 7.56e+00 bond pdb=" N TRP A 227 " pdb=" CA TRP A 227 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.30e-02 5.92e+03 7.46e+00 bond pdb=" N TYR b 366 " pdb=" CA TYR b 366 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.18e+00 ... (remaining 10500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 12952 1.47 - 2.95: 1049 2.95 - 4.42: 225 4.42 - 5.89: 41 5.89 - 7.37: 7 Bond angle restraints: 14274 Sorted by residual: angle pdb=" N CYS A 231 " pdb=" CA CYS A 231 " pdb=" CB CYS A 231 " ideal model delta sigma weight residual 109.94 116.30 -6.36 1.60e+00 3.91e-01 1.58e+01 angle pdb=" CA GLU A 228 " pdb=" C GLU A 228 " pdb=" O GLU A 228 " ideal model delta sigma weight residual 121.23 117.01 4.22 1.07e+00 8.73e-01 1.56e+01 angle pdb=" CA ASN c 365 " pdb=" CB ASN c 365 " pdb=" CG ASN c 365 " ideal model delta sigma weight residual 112.60 116.54 -3.94 1.00e+00 1.00e+00 1.55e+01 angle pdb=" N ASN a 365 " pdb=" CA ASN a 365 " pdb=" C ASN a 365 " ideal model delta sigma weight residual 112.92 108.08 4.84 1.23e+00 6.61e-01 1.55e+01 angle pdb=" N PHE A 233 " pdb=" CA PHE A 233 " pdb=" C PHE A 233 " ideal model delta sigma weight residual 113.55 108.61 4.94 1.26e+00 6.30e-01 1.54e+01 ... (remaining 14269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.15: 6844 21.15 - 42.29: 204 42.29 - 63.44: 54 63.44 - 84.59: 42 84.59 - 105.74: 21 Dihedral angle restraints: 7165 sinusoidal: 3465 harmonic: 3700 Sorted by residual: dihedral pdb=" CB CYS C 207 " pdb=" SG CYS C 207 " pdb=" SG CYS c 360 " pdb=" CB CYS c 360 " ideal model delta sinusoidal sigma weight residual -86.00 -148.40 62.40 1 1.00e+01 1.00e-02 5.15e+01 dihedral pdb=" CB CYS A 86 " pdb=" SG CYS A 86 " pdb=" SG CYS A 231 " pdb=" CB CYS A 231 " ideal model delta sinusoidal sigma weight residual 93.00 142.14 -49.14 1 1.00e+01 1.00e-02 3.32e+01 dihedral pdb=" CB CYS A 180 " pdb=" SG CYS A 180 " pdb=" SG CYS A 212 " pdb=" CB CYS A 212 " ideal model delta sinusoidal sigma weight residual 93.00 46.73 46.27 1 1.00e+01 1.00e-02 2.96e+01 ... (remaining 7162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1731 0.088 - 0.177: 88 0.177 - 0.265: 13 0.265 - 0.353: 0 0.353 - 0.441: 1 Chirality restraints: 1833 Sorted by residual: chirality pdb=" C1 MAN N 5 " pdb=" O2 MAN N 4 " pdb=" C2 MAN N 5 " pdb=" O5 MAN N 5 " both_signs ideal model delta sigma weight residual False 2.40 1.96 0.44 2.00e-02 2.50e+03 4.87e+02 chirality pdb=" C1 MAN N 4 " pdb=" O3 BMA N 3 " pdb=" C2 MAN N 4 " pdb=" O5 MAN N 4 " both_signs ideal model delta sigma weight residual False 2.40 2.23 0.17 2.00e-02 2.50e+03 7.13e+01 chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.77e+01 ... (remaining 1830 not shown) Planarity restraints: 1767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " -0.237 2.00e-02 2.50e+03 1.97e-01 4.86e+02 pdb=" C7 NAG N 1 " 0.064 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " -0.166 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " 0.326 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 701 " -0.117 2.00e-02 2.50e+03 9.67e-02 1.17e+02 pdb=" C7 NAG a 701 " 0.029 2.00e-02 2.50e+03 pdb=" C8 NAG a 701 " -0.087 2.00e-02 2.50e+03 pdb=" N2 NAG a 701 " 0.157 2.00e-02 2.50e+03 pdb=" O7 NAG a 701 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 1 " -0.114 2.00e-02 2.50e+03 9.49e-02 1.13e+02 pdb=" C7 NAG Y 1 " 0.030 2.00e-02 2.50e+03 pdb=" C8 NAG Y 1 " -0.085 2.00e-02 2.50e+03 pdb=" N2 NAG Y 1 " 0.154 2.00e-02 2.50e+03 pdb=" O7 NAG Y 1 " 0.016 2.00e-02 2.50e+03 ... (remaining 1764 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 452 2.73 - 3.27: 10155 3.27 - 3.81: 16591 3.81 - 4.36: 21142 4.36 - 4.90: 35540 Nonbonded interactions: 83880 Sorted by model distance: nonbonded pdb=" OH TYR C 62 " pdb=" OE2 GLU c 396 " model vdw 2.184 3.040 nonbonded pdb=" O ALA C 195 " pdb=" OG SER C 199 " model vdw 2.198 3.040 nonbonded pdb=" O ALA B 195 " pdb=" OG SER B 199 " model vdw 2.215 3.040 nonbonded pdb=" OG1 THR B 81 " pdb=" OD1 ASN b 319 " model vdw 2.220 3.040 nonbonded pdb=" ND2 ASN B 148 " pdb=" OD1 ASN C 127 " model vdw 2.252 3.120 ... (remaining 83875 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 60 through 259 or resid 301)) selection = chain 'B' selection = (chain 'C' and (resid 60 through 259 or resid 301)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'U' } ncs_group { reference = (chain 'F' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) } ncs_group { reference = (chain 'H' and resid 15 through 113) selection = chain 'L' } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = (chain 'a' and (resid 260 through 413 or resid 701 through 702)) selection = chain 'b' selection = (chain 'c' and (resid 260 through 413 or resid 701 through 702)) } 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: 7.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.830 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 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:14.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 : 0.010 0.744 10595 Z= 0.506 Angle : 1.106 59.895 14523 Z= 0.567 Chirality : 0.047 0.441 1833 Planarity : 0.009 0.197 1734 Dihedral : 13.863 105.737 4702 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 1017 helix: 0.29 (0.29), residues: 330 sheet: 0.02 (0.46), residues: 120 loop : -0.13 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 210 HIS 0.007 0.002 HIS A 93 PHE 0.014 0.002 PHE B 157 TYR 0.018 0.002 TYR B 66 ARG 0.006 0.001 ARG A 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 33) link_NAG-ASN : angle 2.35124 ( 99) link_ALPHA1-6 : bond 0.00639 ( 1) link_ALPHA1-6 : angle 1.24007 ( 3) link_BETA1-4 : bond 0.00510 ( 25) link_BETA1-4 : angle 2.09286 ( 75) link_ALPHA1-2 : bond 0.01012 ( 1) link_ALPHA1-2 : angle 3.46242 ( 3) link_ALPHA1-3 : bond 0.00625 ( 4) link_ALPHA1-3 : angle 1.65796 ( 12) hydrogen bonds : bond 0.15371 ( 410) hydrogen bonds : angle 6.25342 ( 1107) link_BETA1-6 : bond 0.00333 ( 5) link_BETA1-6 : angle 1.42930 ( 15) SS BOND : bond 0.18511 ( 21) SS BOND : angle 10.51232 ( 42) covalent geometry : bond 0.00561 (10505) covalent geometry : angle 0.92216 (14274) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: B 134 MET cc_start: 0.8972 (tpp) cc_final: 0.8554 (tpt) REVERT: C 256 ARG cc_start: 0.7774 (mtm-85) cc_final: 0.6957 (mtp85) REVERT: a 270 GLU cc_start: 0.6135 (mm-30) cc_final: 0.4068 (tm-30) REVERT: a 282 ARG cc_start: 0.8093 (ttp-110) cc_final: 0.7812 (ttp-170) REVERT: a 401 ASP cc_start: 0.8924 (m-30) cc_final: 0.8652 (m-30) REVERT: b 379 ARG cc_start: 0.7847 (ttm170) cc_final: 0.7500 (ttp-110) REVERT: c 379 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7668 (ttp-110) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 1.5339 time to fit residues: 331.4920 Evaluate side-chains 166 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 HIS ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 GLN C 92 HIS C 209 ASN C 247 GLN b 295 ASN b 321 GLN c 354 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.149474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.131445 restraints weight = 11261.125| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.66 r_work: 0.3301 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10595 Z= 0.142 Angle : 0.629 6.623 14523 Z= 0.301 Chirality : 0.040 0.166 1833 Planarity : 0.004 0.045 1734 Dihedral : 9.251 78.320 2743 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.83 % Allowed : 6.88 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 1017 helix: 0.35 (0.28), residues: 336 sheet: 0.25 (0.43), residues: 138 loop : 0.17 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 210 HIS 0.006 0.001 HIS A 230 PHE 0.008 0.001 PHE b 399 TYR 0.011 0.001 TYR c 393 ARG 0.006 0.001 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 33) link_NAG-ASN : angle 2.06905 ( 99) link_ALPHA1-6 : bond 0.00230 ( 1) link_ALPHA1-6 : angle 1.97275 ( 3) link_BETA1-4 : bond 0.00377 ( 25) link_BETA1-4 : angle 2.05922 ( 75) link_ALPHA1-2 : bond 0.00813 ( 1) link_ALPHA1-2 : angle 1.69111 ( 3) link_ALPHA1-3 : bond 0.01156 ( 4) link_ALPHA1-3 : angle 1.22695 ( 12) hydrogen bonds : bond 0.03993 ( 410) hydrogen bonds : angle 4.80507 ( 1107) link_BETA1-6 : bond 0.00348 ( 5) link_BETA1-6 : angle 1.30244 ( 15) SS BOND : bond 0.00796 ( 21) SS BOND : angle 0.97905 ( 42) covalent geometry : bond 0.00320 (10505) covalent geometry : angle 0.58586 (14274) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8132 (mttt) REVERT: C 256 ARG cc_start: 0.8017 (mtm-85) cc_final: 0.6803 (mtp180) REVERT: a 282 ARG cc_start: 0.8503 (ttp-110) cc_final: 0.8029 (ttp-170) REVERT: a 332 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7676 (ttt) REVERT: c 339 LYS cc_start: 0.8759 (ptpp) cc_final: 0.8493 (ptmm) REVERT: c 379 ARG cc_start: 0.8263 (ttm-80) cc_final: 0.7392 (ttp-110) outliers start: 17 outliers final: 7 residues processed: 177 average time/residue: 1.4202 time to fit residues: 267.6475 Evaluate side-chains 171 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 367 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 42 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 119 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 114 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN B 189 GLN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 342 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.147543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.129145 restraints weight = 11287.201| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.73 r_work: 0.3288 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10595 Z= 0.125 Angle : 0.580 7.267 14523 Z= 0.278 Chirality : 0.038 0.175 1833 Planarity : 0.003 0.046 1734 Dihedral : 6.942 65.646 2743 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.15 % Allowed : 8.28 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.27), residues: 1017 helix: 0.52 (0.29), residues: 336 sheet: 0.43 (0.43), residues: 138 loop : 0.19 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 210 HIS 0.004 0.001 HIS C 230 PHE 0.007 0.001 PHE b 399 TYR 0.010 0.001 TYR B 200 ARG 0.007 0.000 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 33) link_NAG-ASN : angle 2.04654 ( 99) link_ALPHA1-6 : bond 0.00310 ( 1) link_ALPHA1-6 : angle 1.69950 ( 3) link_BETA1-4 : bond 0.00364 ( 25) link_BETA1-4 : angle 1.89281 ( 75) link_ALPHA1-2 : bond 0.01122 ( 1) link_ALPHA1-2 : angle 1.57047 ( 3) link_ALPHA1-3 : bond 0.01092 ( 4) link_ALPHA1-3 : angle 1.16972 ( 12) hydrogen bonds : bond 0.03561 ( 410) hydrogen bonds : angle 4.51768 ( 1107) link_BETA1-6 : bond 0.00305 ( 5) link_BETA1-6 : angle 1.31815 ( 15) SS BOND : bond 0.00435 ( 21) SS BOND : angle 0.72583 ( 42) covalent geometry : bond 0.00281 (10505) covalent geometry : angle 0.53782 (14274) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8790 (p0) cc_final: 0.8514 (p0) REVERT: B 134 MET cc_start: 0.9243 (tpp) cc_final: 0.8762 (tpt) REVERT: C 256 ARG cc_start: 0.7972 (mtm-85) cc_final: 0.6683 (mtp85) REVERT: a 270 GLU cc_start: 0.5863 (mm-30) cc_final: 0.3562 (tm-30) REVERT: a 282 ARG cc_start: 0.8498 (ttp-110) cc_final: 0.7977 (ttp-170) REVERT: a 332 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7773 (ttt) REVERT: c 379 ARG cc_start: 0.8204 (ttm-80) cc_final: 0.7233 (ttp-110) outliers start: 20 outliers final: 8 residues processed: 178 average time/residue: 1.3826 time to fit residues: 262.4043 Evaluate side-chains 167 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 158 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 367 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 66 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.141133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.122562 restraints weight = 11328.311| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.74 r_work: 0.3198 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10595 Z= 0.196 Angle : 0.661 7.791 14523 Z= 0.313 Chirality : 0.041 0.198 1833 Planarity : 0.004 0.045 1734 Dihedral : 6.805 62.818 2743 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.12 % Allowed : 8.17 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.26), residues: 1017 helix: 0.34 (0.28), residues: 336 sheet: 0.33 (0.43), residues: 138 loop : 0.16 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 210 HIS 0.007 0.001 HIS C 230 PHE 0.011 0.002 PHE b 399 TYR 0.014 0.002 TYR B 66 ARG 0.007 0.001 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 33) link_NAG-ASN : angle 2.27444 ( 99) link_ALPHA1-6 : bond 0.00231 ( 1) link_ALPHA1-6 : angle 1.70789 ( 3) link_BETA1-4 : bond 0.00332 ( 25) link_BETA1-4 : angle 2.12484 ( 75) link_ALPHA1-2 : bond 0.00861 ( 1) link_ALPHA1-2 : angle 1.95979 ( 3) link_ALPHA1-3 : bond 0.00909 ( 4) link_ALPHA1-3 : angle 1.27659 ( 12) hydrogen bonds : bond 0.04028 ( 410) hydrogen bonds : angle 4.69699 ( 1107) link_BETA1-6 : bond 0.00237 ( 5) link_BETA1-6 : angle 1.46917 ( 15) SS BOND : bond 0.00454 ( 21) SS BOND : angle 0.85720 ( 42) covalent geometry : bond 0.00461 (10505) covalent geometry : angle 0.61463 (14274) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8826 (p0) cc_final: 0.8556 (p0) REVERT: A 116 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.7936 (mttt) REVERT: A 125 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8287 (tptp) REVERT: C 114 ASN cc_start: 0.8254 (p0) cc_final: 0.7669 (t160) REVERT: C 256 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.6751 (mtp85) REVERT: a 270 GLU cc_start: 0.5902 (mm-30) cc_final: 0.3521 (tm-30) REVERT: a 282 ARG cc_start: 0.8513 (ttp-110) cc_final: 0.7934 (ttp-170) REVERT: a 332 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7873 (ttt) REVERT: c 379 ARG cc_start: 0.8208 (ttm-80) cc_final: 0.7257 (ttp-110) REVERT: c 396 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7517 (tt0) outliers start: 29 outliers final: 13 residues processed: 177 average time/residue: 1.4227 time to fit residues: 268.0143 Evaluate side-chains 179 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain b residue 265 THR Chi-restraints excluded: chain b residue 404 GLU Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 396 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 87 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 165 GLN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 354 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.138094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.119373 restraints weight = 11368.977| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.77 r_work: 0.3160 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10595 Z= 0.266 Angle : 0.744 8.163 14523 Z= 0.348 Chirality : 0.044 0.204 1833 Planarity : 0.004 0.050 1734 Dihedral : 7.300 64.687 2743 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.87 % Allowed : 8.06 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.26), residues: 1017 helix: -0.12 (0.27), residues: 354 sheet: 0.34 (0.43), residues: 138 loop : 0.01 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 210 HIS 0.008 0.001 HIS C 230 PHE 0.013 0.002 PHE b 399 TYR 0.013 0.002 TYR B 66 ARG 0.007 0.001 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00459 ( 33) link_NAG-ASN : angle 2.52122 ( 99) link_ALPHA1-6 : bond 0.00104 ( 1) link_ALPHA1-6 : angle 1.71865 ( 3) link_BETA1-4 : bond 0.00381 ( 25) link_BETA1-4 : angle 2.32256 ( 75) link_ALPHA1-2 : bond 0.00839 ( 1) link_ALPHA1-2 : angle 2.28838 ( 3) link_ALPHA1-3 : bond 0.00768 ( 4) link_ALPHA1-3 : angle 1.34327 ( 12) hydrogen bonds : bond 0.04529 ( 410) hydrogen bonds : angle 4.90354 ( 1107) link_BETA1-6 : bond 0.00263 ( 5) link_BETA1-6 : angle 1.62538 ( 15) SS BOND : bond 0.00529 ( 21) SS BOND : angle 1.03551 ( 42) covalent geometry : bond 0.00635 (10505) covalent geometry : angle 0.69421 (14274) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.7896 (mttt) REVERT: A 125 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8307 (tptp) REVERT: B 134 MET cc_start: 0.9288 (tpp) cc_final: 0.8856 (tpt) REVERT: C 114 ASN cc_start: 0.8266 (p0) cc_final: 0.7582 (t160) REVERT: C 116 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8426 (mttt) REVERT: C 256 ARG cc_start: 0.8173 (mtm-85) cc_final: 0.6782 (mtp180) REVERT: a 270 GLU cc_start: 0.5952 (mm-30) cc_final: 0.3465 (tm-30) REVERT: a 282 ARG cc_start: 0.8513 (ttp-110) cc_final: 0.8038 (ttp-170) REVERT: a 332 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7819 (ttt) REVERT: c 379 ARG cc_start: 0.8257 (ttm-80) cc_final: 0.7268 (ttp-110) REVERT: c 396 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.7702 (tt0) outliers start: 36 outliers final: 21 residues processed: 177 average time/residue: 1.4385 time to fit residues: 271.9778 Evaluate side-chains 183 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain a residue 392 SER Chi-restraints excluded: chain b residue 404 GLU Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 396 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 116 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.142016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.123488 restraints weight = 11440.358| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.75 r_work: 0.3218 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10595 Z= 0.144 Angle : 0.609 6.773 14523 Z= 0.290 Chirality : 0.039 0.190 1833 Planarity : 0.003 0.048 1734 Dihedral : 6.519 59.465 2743 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.01 % Allowed : 10.22 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.27), residues: 1017 helix: 0.40 (0.28), residues: 336 sheet: 0.43 (0.43), residues: 138 loop : 0.09 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 210 HIS 0.004 0.001 HIS A 115 PHE 0.008 0.001 PHE b 399 TYR 0.010 0.001 TYR B 200 ARG 0.007 0.000 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 33) link_NAG-ASN : angle 2.26753 ( 99) link_ALPHA1-6 : bond 0.00468 ( 1) link_ALPHA1-6 : angle 1.58242 ( 3) link_BETA1-4 : bond 0.00340 ( 25) link_BETA1-4 : angle 1.95361 ( 75) link_ALPHA1-2 : bond 0.00911 ( 1) link_ALPHA1-2 : angle 1.80803 ( 3) link_ALPHA1-3 : bond 0.00992 ( 4) link_ALPHA1-3 : angle 1.23512 ( 12) hydrogen bonds : bond 0.03647 ( 410) hydrogen bonds : angle 4.59038 ( 1107) link_BETA1-6 : bond 0.00268 ( 5) link_BETA1-6 : angle 1.38499 ( 15) SS BOND : bond 0.00438 ( 21) SS BOND : angle 1.28718 ( 42) covalent geometry : bond 0.00333 (10505) covalent geometry : angle 0.55856 (14274) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7870 (mttt) REVERT: A 125 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8248 (tptp) REVERT: A 192 MET cc_start: 0.8533 (ptm) cc_final: 0.8159 (ppp) REVERT: B 134 MET cc_start: 0.9225 (tpp) cc_final: 0.8695 (tpt) REVERT: C 95 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8650 (tt) REVERT: C 256 ARG cc_start: 0.8067 (mtm-85) cc_final: 0.6755 (mtp85) REVERT: a 270 GLU cc_start: 0.5966 (mm-30) cc_final: 0.3540 (tm-30) REVERT: a 282 ARG cc_start: 0.8515 (ttp-110) cc_final: 0.7906 (ttp-170) REVERT: c 379 ARG cc_start: 0.8216 (ttm-80) cc_final: 0.7283 (ttp-110) REVERT: c 396 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7623 (tt0) outliers start: 28 outliers final: 19 residues processed: 175 average time/residue: 1.7487 time to fit residues: 324.9493 Evaluate side-chains 178 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain b residue 404 GLU Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 396 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 45 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.141180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.122653 restraints weight = 11486.066| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.75 r_work: 0.3206 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10595 Z= 0.174 Angle : 0.633 6.995 14523 Z= 0.300 Chirality : 0.040 0.202 1833 Planarity : 0.003 0.048 1734 Dihedral : 6.429 58.453 2743 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.23 % Allowed : 10.11 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.27), residues: 1017 helix: 0.40 (0.28), residues: 336 sheet: 0.54 (0.44), residues: 138 loop : 0.08 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 210 HIS 0.005 0.001 HIS C 230 PHE 0.010 0.002 PHE b 399 TYR 0.011 0.001 TYR A 66 ARG 0.008 0.001 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 33) link_NAG-ASN : angle 2.29263 ( 99) link_ALPHA1-6 : bond 0.00437 ( 1) link_ALPHA1-6 : angle 1.56938 ( 3) link_BETA1-4 : bond 0.00323 ( 25) link_BETA1-4 : angle 2.04981 ( 75) link_ALPHA1-2 : bond 0.00899 ( 1) link_ALPHA1-2 : angle 1.91645 ( 3) link_ALPHA1-3 : bond 0.00910 ( 4) link_ALPHA1-3 : angle 1.29040 ( 12) hydrogen bonds : bond 0.03834 ( 410) hydrogen bonds : angle 4.58317 ( 1107) link_BETA1-6 : bond 0.00237 ( 5) link_BETA1-6 : angle 1.45740 ( 15) SS BOND : bond 0.00350 ( 21) SS BOND : angle 1.25482 ( 42) covalent geometry : bond 0.00406 (10505) covalent geometry : angle 0.58277 (14274) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8786 (p0) cc_final: 0.8519 (p0) REVERT: A 116 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.7888 (mttt) REVERT: A 125 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8295 (tptp) REVERT: B 134 MET cc_start: 0.9247 (tpp) cc_final: 0.8782 (tpt) REVERT: C 116 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8398 (mttt) REVERT: C 256 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.6757 (mtp85) REVERT: a 270 GLU cc_start: 0.5908 (mm-30) cc_final: 0.3448 (tm-30) REVERT: a 282 ARG cc_start: 0.8515 (ttp-110) cc_final: 0.7906 (ttp-170) REVERT: c 379 ARG cc_start: 0.8226 (ttm-80) cc_final: 0.7358 (ttp-110) outliers start: 30 outliers final: 21 residues processed: 172 average time/residue: 1.5701 time to fit residues: 286.9548 Evaluate side-chains 178 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 404 GLU Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 341 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 23 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 33 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 114 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 118 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.141145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.122566 restraints weight = 11486.584| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.75 r_work: 0.3205 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10595 Z= 0.178 Angle : 0.631 7.002 14523 Z= 0.300 Chirality : 0.040 0.205 1833 Planarity : 0.003 0.047 1734 Dihedral : 6.375 57.751 2743 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.90 % Allowed : 10.32 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.27), residues: 1017 helix: 0.40 (0.28), residues: 336 sheet: 0.55 (0.44), residues: 138 loop : 0.08 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 210 HIS 0.005 0.001 HIS C 230 PHE 0.010 0.002 PHE b 399 TYR 0.025 0.002 TYR A 66 ARG 0.009 0.001 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 33) link_NAG-ASN : angle 2.28318 ( 99) link_ALPHA1-6 : bond 0.00470 ( 1) link_ALPHA1-6 : angle 1.55546 ( 3) link_BETA1-4 : bond 0.00329 ( 25) link_BETA1-4 : angle 2.03296 ( 75) link_ALPHA1-2 : bond 0.00870 ( 1) link_ALPHA1-2 : angle 1.92347 ( 3) link_ALPHA1-3 : bond 0.00924 ( 4) link_ALPHA1-3 : angle 1.28993 ( 12) hydrogen bonds : bond 0.03832 ( 410) hydrogen bonds : angle 4.57507 ( 1107) link_BETA1-6 : bond 0.00231 ( 5) link_BETA1-6 : angle 1.45419 ( 15) SS BOND : bond 0.00431 ( 21) SS BOND : angle 1.35276 ( 42) covalent geometry : bond 0.00417 (10505) covalent geometry : angle 0.58102 (14274) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8780 (p0) cc_final: 0.8504 (p0) REVERT: A 116 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.7848 (mttt) REVERT: A 125 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8296 (tptp) REVERT: B 134 MET cc_start: 0.9244 (tpp) cc_final: 0.8775 (tpt) REVERT: C 116 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8396 (mttt) REVERT: C 256 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.6752 (mtp85) REVERT: a 270 GLU cc_start: 0.5900 (mm-30) cc_final: 0.3447 (tm-30) REVERT: a 282 ARG cc_start: 0.8500 (ttp-110) cc_final: 0.7953 (ttp-170) REVERT: b 331 GLN cc_start: 0.7349 (tp-100) cc_final: 0.6034 (tt0) REVERT: b 339 LYS cc_start: 0.8704 (pttt) cc_final: 0.8439 (pttt) REVERT: c 379 ARG cc_start: 0.8205 (ttm-80) cc_final: 0.7350 (ttp-110) outliers start: 27 outliers final: 22 residues processed: 171 average time/residue: 1.7333 time to fit residues: 316.7673 Evaluate side-chains 181 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 404 GLU Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 341 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.0470 chunk 101 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 42 optimal weight: 0.0970 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 354 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.142771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.124373 restraints weight = 11530.228| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.75 r_work: 0.3236 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10595 Z= 0.132 Angle : 0.588 7.463 14523 Z= 0.282 Chirality : 0.038 0.203 1833 Planarity : 0.003 0.045 1734 Dihedral : 5.998 54.302 2743 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.80 % Allowed : 10.65 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.27), residues: 1017 helix: 0.64 (0.28), residues: 333 sheet: 0.60 (0.44), residues: 138 loop : 0.14 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 210 HIS 0.006 0.001 HIS C 179 PHE 0.007 0.001 PHE b 399 TYR 0.021 0.001 TYR A 66 ARG 0.009 0.000 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00199 ( 33) link_NAG-ASN : angle 2.16467 ( 99) link_ALPHA1-6 : bond 0.00637 ( 1) link_ALPHA1-6 : angle 1.50837 ( 3) link_BETA1-4 : bond 0.00334 ( 25) link_BETA1-4 : angle 1.86402 ( 75) link_ALPHA1-2 : bond 0.00925 ( 1) link_ALPHA1-2 : angle 1.71875 ( 3) link_ALPHA1-3 : bond 0.01001 ( 4) link_ALPHA1-3 : angle 1.23179 ( 12) hydrogen bonds : bond 0.03477 ( 410) hydrogen bonds : angle 4.42680 ( 1107) link_BETA1-6 : bond 0.00266 ( 5) link_BETA1-6 : angle 1.35720 ( 15) SS BOND : bond 0.00425 ( 21) SS BOND : angle 1.44254 ( 42) covalent geometry : bond 0.00301 (10505) covalent geometry : angle 0.53912 (14274) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8756 (p0) cc_final: 0.8504 (p0) REVERT: A 116 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.7851 (mttt) REVERT: A 192 MET cc_start: 0.8555 (ptm) cc_final: 0.8202 (ppp) REVERT: B 134 MET cc_start: 0.9225 (tpp) cc_final: 0.8736 (tpt) REVERT: C 95 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8665 (tt) REVERT: C 256 ARG cc_start: 0.8057 (mtm-85) cc_final: 0.6774 (mtp85) REVERT: a 270 GLU cc_start: 0.5890 (mm-30) cc_final: 0.3443 (tm-30) REVERT: a 282 ARG cc_start: 0.8477 (ttp-110) cc_final: 0.7934 (ttp-170) REVERT: b 331 GLN cc_start: 0.7378 (tp-100) cc_final: 0.6052 (tt0) REVERT: b 339 LYS cc_start: 0.8635 (pttt) cc_final: 0.8409 (pttt) REVERT: b 379 ARG cc_start: 0.8212 (ttp80) cc_final: 0.7356 (ttp80) REVERT: c 303 GLU cc_start: 0.7979 (mp0) cc_final: 0.7653 (mt-10) REVERT: c 379 ARG cc_start: 0.8209 (ttm-80) cc_final: 0.7393 (ttp-110) outliers start: 26 outliers final: 21 residues processed: 179 average time/residue: 1.7025 time to fit residues: 324.1788 Evaluate side-chains 183 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 404 GLU Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 41 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 28 optimal weight: 0.0030 chunk 20 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 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 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.140671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.122410 restraints weight = 11527.415| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.72 r_work: 0.3227 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10595 Z= 0.128 Angle : 0.610 14.457 14523 Z= 0.292 Chirality : 0.039 0.318 1833 Planarity : 0.003 0.044 1734 Dihedral : 5.897 52.493 2743 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.37 % Allowed : 11.40 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.35 (0.27), residues: 1017 helix: 0.64 (0.28), residues: 339 sheet: 0.64 (0.45), residues: 138 loop : -0.03 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 210 HIS 0.004 0.001 HIS C 230 PHE 0.007 0.001 PHE b 399 TYR 0.024 0.001 TYR A 66 ARG 0.010 0.000 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 33) link_NAG-ASN : angle 2.14244 ( 99) link_ALPHA1-6 : bond 0.00670 ( 1) link_ALPHA1-6 : angle 1.46004 ( 3) link_BETA1-4 : bond 0.00330 ( 25) link_BETA1-4 : angle 1.84219 ( 75) link_ALPHA1-2 : bond 0.00853 ( 1) link_ALPHA1-2 : angle 1.68903 ( 3) link_ALPHA1-3 : bond 0.00974 ( 4) link_ALPHA1-3 : angle 1.24189 ( 12) hydrogen bonds : bond 0.03401 ( 410) hydrogen bonds : angle 4.36367 ( 1107) link_BETA1-6 : bond 0.00276 ( 5) link_BETA1-6 : angle 1.36046 ( 15) SS BOND : bond 0.00364 ( 21) SS BOND : angle 2.32558 ( 42) covalent geometry : bond 0.00290 (10505) covalent geometry : angle 0.55527 (14274) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8721 (p0) cc_final: 0.8468 (p0) REVERT: A 116 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7847 (mttt) REVERT: A 192 MET cc_start: 0.8529 (ptm) cc_final: 0.8207 (ppp) REVERT: B 134 MET cc_start: 0.9208 (tpp) cc_final: 0.8712 (tpt) REVERT: C 95 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8643 (tt) REVERT: C 256 ARG cc_start: 0.8025 (mtm-85) cc_final: 0.6766 (mtp85) REVERT: a 270 GLU cc_start: 0.5882 (mm-30) cc_final: 0.3468 (tm-30) REVERT: a 282 ARG cc_start: 0.8427 (ttp-110) cc_final: 0.7878 (ttp-170) REVERT: b 379 ARG cc_start: 0.8192 (ttp80) cc_final: 0.7340 (ttp80) REVERT: c 303 GLU cc_start: 0.7993 (mp0) cc_final: 0.7660 (mt-10) REVERT: c 379 ARG cc_start: 0.8223 (ttm-80) cc_final: 0.7327 (ttp-110) outliers start: 22 outliers final: 20 residues processed: 170 average time/residue: 1.5988 time to fit residues: 288.4870 Evaluate side-chains 176 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 404 GLU Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 50 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.139076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.120586 restraints weight = 11551.189| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.75 r_work: 0.3181 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10595 Z= 0.263 Angle : 0.748 14.160 14523 Z= 0.351 Chirality : 0.044 0.331 1833 Planarity : 0.004 0.047 1734 Dihedral : 6.731 59.744 2743 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.80 % Allowed : 10.97 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.27), residues: 1017 helix: 0.03 (0.27), residues: 354 sheet: 0.56 (0.45), residues: 138 loop : -0.01 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 210 HIS 0.005 0.001 HIS A 115 PHE 0.013 0.002 PHE b 399 TYR 0.028 0.002 TYR A 66 ARG 0.013 0.001 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 33) link_NAG-ASN : angle 2.44776 ( 99) link_ALPHA1-6 : bond 0.00314 ( 1) link_ALPHA1-6 : angle 1.56170 ( 3) link_BETA1-4 : bond 0.00368 ( 25) link_BETA1-4 : angle 2.24750 ( 75) link_ALPHA1-2 : bond 0.00649 ( 1) link_ALPHA1-2 : angle 2.23602 ( 3) link_ALPHA1-3 : bond 0.00776 ( 4) link_ALPHA1-3 : angle 1.36217 ( 12) hydrogen bonds : bond 0.04353 ( 410) hydrogen bonds : angle 4.74451 ( 1107) link_BETA1-6 : bond 0.00237 ( 5) link_BETA1-6 : angle 1.59573 ( 15) SS BOND : bond 0.00568 ( 21) SS BOND : angle 2.47932 ( 42) covalent geometry : bond 0.00627 (10505) covalent geometry : angle 0.69140 (14274) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8352.91 seconds wall clock time: 146 minutes 51.62 seconds (8811.62 seconds total)