Starting phenix.real_space_refine on Wed Sep 17 18:10:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ve8_43168/09_2025/8ve8_43168.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ve8_43168/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ve8_43168/09_2025/8ve8_43168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ve8_43168/09_2025/8ve8_43168.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ve8_43168/09_2025/8ve8_43168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ve8_43168/09_2025/8ve8_43168.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.81, per 1000 atoms: 0.27 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: 1.35 Conformation dependent library (CDL) restraints added in 363.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.33 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: 1.62 Time building geometry restraints manager: 1.64 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 301) selection = chain 'B' selection = (chain 'C' and resid 60 through 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 702) selection = chain 'b' selection = (chain 'c' and resid 260 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: 9.810 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.990 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.380 ------------------------------------------------------------------------------- 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 : 2.22 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG A 257 TYR 0.018 0.002 TYR B 66 PHE 0.014 0.002 PHE B 157 TRP 0.014 0.001 TRP A 210 HIS 0.007 0.002 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00561 (10505) covalent geometry : angle 0.92216 (14274) SS BOND : bond 0.18511 ( 21) SS BOND : angle 10.51232 ( 42) hydrogen bonds : bond 0.15371 ( 410) hydrogen bonds : angle 6.25342 ( 1107) 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) 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_BETA1-6 : bond 0.00333 ( 5) link_BETA1-6 : angle 1.42930 ( 15) link_NAG-ASN : bond 0.00460 ( 33) link_NAG-ASN : angle 2.35124 ( 99) *********************** 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 : 0.284 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: 0.6796 time to fit residues: 146.6914 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 : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 247 GLN B 92 HIS ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 GLN C 92 HIS C 185 ASN C 209 ASN C 223 GLN C 247 GLN b 295 ASN b 321 GLN c 354 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.145574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.126877 restraints weight = 11415.234| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.74 r_work: 0.3247 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10595 Z= 0.203 Angle : 0.705 7.151 14523 Z= 0.335 Chirality : 0.043 0.174 1833 Planarity : 0.004 0.049 1734 Dihedral : 9.134 77.850 2743 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.04 % Allowed : 6.88 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.26), residues: 1017 helix: 0.12 (0.28), residues: 336 sheet: 0.24 (0.43), residues: 138 loop : 0.11 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 282 TYR 0.012 0.002 TYR c 393 PHE 0.011 0.002 PHE b 399 TRP 0.008 0.001 TRP C 210 HIS 0.008 0.002 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00473 (10505) covalent geometry : angle 0.65923 (14274) SS BOND : bond 0.00682 ( 21) SS BOND : angle 1.18138 ( 42) hydrogen bonds : bond 0.04153 ( 410) hydrogen bonds : angle 4.92014 ( 1107) link_ALPHA1-2 : bond 0.00721 ( 1) link_ALPHA1-2 : angle 2.02814 ( 3) link_ALPHA1-3 : bond 0.01099 ( 4) link_ALPHA1-3 : angle 1.23244 ( 12) link_ALPHA1-6 : bond 0.00321 ( 1) link_ALPHA1-6 : angle 2.10623 ( 3) link_BETA1-4 : bond 0.00405 ( 25) link_BETA1-4 : angle 2.27717 ( 75) link_BETA1-6 : bond 0.00274 ( 5) link_BETA1-6 : angle 1.43399 ( 15) link_NAG-ASN : bond 0.00304 ( 33) link_NAG-ASN : angle 2.24335 ( 99) *********************** 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 187 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8030 (mttt) REVERT: C 256 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.6717 (mtp180) REVERT: a 282 ARG cc_start: 0.8534 (ttp-110) cc_final: 0.8021 (ttp-170) REVERT: a 332 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7634 (ttt) REVERT: c 327 LYS cc_start: 0.8027 (tttt) cc_final: 0.7222 (mmtp) REVERT: c 379 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7259 (ttp-110) outliers start: 19 outliers final: 10 residues processed: 176 average time/residue: 0.6857 time to fit residues: 128.2526 Evaluate side-chains 167 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 214 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 101 THR Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 332 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN ** B 230 HIS ** 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 = 0.3602 r_free = 0.3602 target = 0.144376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.125923 restraints weight = 11284.130| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.72 r_work: 0.3257 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10595 Z= 0.159 Angle : 0.626 7.478 14523 Z= 0.297 Chirality : 0.040 0.173 1833 Planarity : 0.003 0.047 1734 Dihedral : 7.505 68.723 2743 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.69 % Allowed : 7.85 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.26), residues: 1017 helix: 0.28 (0.28), residues: 336 sheet: 0.32 (0.43), residues: 138 loop : 0.17 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 282 TYR 0.011 0.002 TYR A 66 PHE 0.009 0.001 PHE b 399 TRP 0.009 0.001 TRP A 210 HIS 0.005 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00369 (10505) covalent geometry : angle 0.58079 (14274) SS BOND : bond 0.00495 ( 21) SS BOND : angle 0.77357 ( 42) hydrogen bonds : bond 0.03900 ( 410) hydrogen bonds : angle 4.68183 ( 1107) link_ALPHA1-2 : bond 0.01120 ( 1) link_ALPHA1-2 : angle 1.69613 ( 3) link_ALPHA1-3 : bond 0.01061 ( 4) link_ALPHA1-3 : angle 1.24105 ( 12) link_ALPHA1-6 : bond 0.00191 ( 1) link_ALPHA1-6 : angle 1.77211 ( 3) link_BETA1-4 : bond 0.00342 ( 25) link_BETA1-4 : angle 2.03605 ( 75) link_BETA1-6 : bond 0.00256 ( 5) link_BETA1-6 : angle 1.39952 ( 15) link_NAG-ASN : bond 0.00222 ( 33) link_NAG-ASN : angle 2.19676 ( 99) *********************** 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: 25 poor density : 167 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8321 (tptp) REVERT: C 95 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8677 (tt) REVERT: C 256 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.6765 (mtp180) REVERT: a 270 GLU cc_start: 0.5818 (mm-30) cc_final: 0.3543 (tm-30) REVERT: a 282 ARG cc_start: 0.8519 (ttp-110) cc_final: 0.8016 (ttp-170) REVERT: a 332 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7834 (ttt) REVERT: c 379 ARG cc_start: 0.8237 (ttm-80) cc_final: 0.7305 (ttp-110) REVERT: c 396 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7401 (tt0) outliers start: 25 outliers final: 9 residues processed: 175 average time/residue: 0.6933 time to fit residues: 128.6884 Evaluate side-chains 170 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 189 GLN 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 251 ASP Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 396 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 104 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3516 r_free = 0.3516 target = 0.137716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.118969 restraints weight = 11508.549| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.78 r_work: 0.3178 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 10595 Z= 0.295 Angle : 0.777 8.503 14523 Z= 0.361 Chirality : 0.045 0.203 1833 Planarity : 0.004 0.052 1734 Dihedral : 7.736 68.147 2743 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.98 % Allowed : 8.39 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.26), residues: 1017 helix: -0.20 (0.27), residues: 354 sheet: 0.34 (0.43), residues: 138 loop : 0.04 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 282 TYR 0.022 0.002 TYR A 66 PHE 0.014 0.002 PHE b 399 TRP 0.009 0.002 TRP C 210 HIS 0.007 0.001 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00709 (10505) covalent geometry : angle 0.72739 (14274) SS BOND : bond 0.00560 ( 21) SS BOND : angle 1.02963 ( 42) hydrogen bonds : bond 0.04696 ( 410) hydrogen bonds : angle 5.04280 ( 1107) link_ALPHA1-2 : bond 0.00745 ( 1) link_ALPHA1-2 : angle 2.44408 ( 3) link_ALPHA1-3 : bond 0.00748 ( 4) link_ALPHA1-3 : angle 1.38697 ( 12) link_ALPHA1-6 : bond 0.00012 ( 1) link_ALPHA1-6 : angle 1.76970 ( 3) link_BETA1-4 : bond 0.00410 ( 25) link_BETA1-4 : angle 2.40314 ( 75) link_BETA1-6 : bond 0.00289 ( 5) link_BETA1-6 : angle 1.65257 ( 15) link_NAG-ASN : bond 0.00480 ( 33) link_NAG-ASN : angle 2.54483 ( 99) *********************** 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 201 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.7930 (mttt) REVERT: A 125 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8343 (tptp) REVERT: A 192 MET cc_start: 0.8559 (ptm) cc_final: 0.8173 (ppp) REVERT: B 116 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8914 (mttm) REVERT: C 95 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8692 (tp) REVERT: C 114 ASN cc_start: 0.8261 (p0) cc_final: 0.7626 (t160) REVERT: C 116 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8444 (mttt) REVERT: C 256 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.6850 (mtp180) REVERT: a 270 GLU cc_start: 0.6076 (mm-30) cc_final: 0.3507 (tm-30) REVERT: a 282 ARG cc_start: 0.8488 (ttp-110) cc_final: 0.7924 (ttp-170) REVERT: a 332 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.7881 (ttt) REVERT: c 303 GLU cc_start: 0.8082 (mp0) cc_final: 0.7877 (mt-10) REVERT: c 379 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.7379 (ttp-110) REVERT: c 396 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7719 (tt0) outliers start: 37 outliers final: 21 residues processed: 183 average time/residue: 0.6924 time to fit residues: 134.5481 Evaluate side-chains 184 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 189 GLN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 LYS 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 5 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 b 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.143942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.125405 restraints weight = 11460.628| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.75 r_work: 0.3248 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10595 Z= 0.115 Angle : 0.578 6.612 14523 Z= 0.277 Chirality : 0.037 0.185 1833 Planarity : 0.003 0.047 1734 Dihedral : 6.508 59.139 2743 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.69 % Allowed : 10.97 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.27), residues: 1017 helix: 0.48 (0.28), residues: 336 sheet: 0.52 (0.43), residues: 138 loop : 0.11 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 282 TYR 0.016 0.001 TYR A 66 PHE 0.009 0.001 PHE B 157 TRP 0.010 0.001 TRP A 210 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00253 (10505) covalent geometry : angle 0.53091 (14274) SS BOND : bond 0.00342 ( 21) SS BOND : angle 1.12601 ( 42) hydrogen bonds : bond 0.03384 ( 410) hydrogen bonds : angle 4.54949 ( 1107) link_ALPHA1-2 : bond 0.01057 ( 1) link_ALPHA1-2 : angle 1.64093 ( 3) link_ALPHA1-3 : bond 0.01209 ( 4) link_ALPHA1-3 : angle 1.17933 ( 12) link_ALPHA1-6 : bond 0.00556 ( 1) link_ALPHA1-6 : angle 1.55565 ( 3) link_BETA1-4 : bond 0.00385 ( 25) link_BETA1-4 : angle 1.81684 ( 75) link_BETA1-6 : bond 0.00301 ( 5) link_BETA1-6 : angle 1.31709 ( 15) link_NAG-ASN : bond 0.00177 ( 33) link_NAG-ASN : angle 2.18927 ( 99) *********************** 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 195 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.7833 (mttt) REVERT: A 192 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8174 (ppp) REVERT: B 116 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8916 (mttm) REVERT: B 134 MET cc_start: 0.9220 (tpp) cc_final: 0.8725 (tpt) REVERT: C 95 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8703 (tt) REVERT: C 256 ARG cc_start: 0.8073 (mtm-85) cc_final: 0.6791 (mtp85) REVERT: a 270 GLU cc_start: 0.5804 (mm-30) cc_final: 0.3442 (tm-30) REVERT: a 282 ARG cc_start: 0.8473 (ttp-110) cc_final: 0.7911 (ttp-170) REVERT: b 379 ARG cc_start: 0.8191 (ttp80) cc_final: 0.7893 (ttp-110) REVERT: c 379 ARG cc_start: 0.8230 (ttm-80) cc_final: 0.7323 (ttp-110) REVERT: c 396 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7572 (tt0) outliers start: 25 outliers final: 13 residues processed: 180 average time/residue: 0.7158 time to fit residues: 136.8132 Evaluate side-chains 175 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 116 LYS 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 61 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 251 ASP 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 396 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 41 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 75 optimal weight: 0.2980 chunk 93 optimal weight: 0.0370 overall best weight: 0.7860 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.143063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.124633 restraints weight = 11600.069| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.76 r_work: 0.3242 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10595 Z= 0.134 Angle : 0.588 7.020 14523 Z= 0.280 Chirality : 0.038 0.197 1833 Planarity : 0.003 0.045 1734 Dihedral : 6.298 57.533 2743 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.01 % Allowed : 10.97 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.27), residues: 1017 helix: 0.47 (0.28), residues: 342 sheet: 0.55 (0.43), residues: 138 loop : -0.00 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 282 TYR 0.014 0.001 TYR A 66 PHE 0.008 0.001 PHE b 399 TRP 0.010 0.001 TRP A 210 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00309 (10505) covalent geometry : angle 0.54052 (14274) SS BOND : bond 0.00301 ( 21) SS BOND : angle 1.08151 ( 42) hydrogen bonds : bond 0.03469 ( 410) hydrogen bonds : angle 4.48586 ( 1107) link_ALPHA1-2 : bond 0.00973 ( 1) link_ALPHA1-2 : angle 1.72550 ( 3) link_ALPHA1-3 : bond 0.01047 ( 4) link_ALPHA1-3 : angle 1.21451 ( 12) link_ALPHA1-6 : bond 0.00521 ( 1) link_ALPHA1-6 : angle 1.55667 ( 3) link_BETA1-4 : bond 0.00336 ( 25) link_BETA1-4 : angle 1.89223 ( 75) link_BETA1-6 : bond 0.00270 ( 5) link_BETA1-6 : angle 1.36476 ( 15) link_NAG-ASN : bond 0.00203 ( 33) link_NAG-ASN : angle 2.17406 ( 99) *********************** 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 : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.7858 (mttt) REVERT: A 125 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8282 (tptp) REVERT: A 192 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8173 (ppp) REVERT: B 116 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8911 (mttm) REVERT: B 134 MET cc_start: 0.9231 (tpp) cc_final: 0.8743 (tpt) REVERT: C 95 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8680 (tt) REVERT: C 116 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8422 (mttm) REVERT: C 256 ARG cc_start: 0.8069 (mtm-85) cc_final: 0.6793 (mtp85) REVERT: a 270 GLU cc_start: 0.5881 (mm-30) cc_final: 0.3461 (tm-30) REVERT: a 282 ARG cc_start: 0.8477 (ttp-110) cc_final: 0.7963 (ttp-170) REVERT: b 379 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7908 (ttp-110) REVERT: c 379 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.7344 (ttp-110) REVERT: c 396 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7623 (tt0) outliers start: 28 outliers final: 17 residues processed: 175 average time/residue: 0.7343 time to fit residues: 136.4984 Evaluate side-chains 183 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 189 GLN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain B residue 116 LYS 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 61 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 251 ASP 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 388 VAL 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 65 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 chunk 99 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** 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 = 0.3594 r_free = 0.3594 target = 0.143844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.125487 restraints weight = 11348.650| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.75 r_work: 0.3251 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10595 Z= 0.123 Angle : 0.564 6.929 14523 Z= 0.270 Chirality : 0.037 0.205 1833 Planarity : 0.003 0.044 1734 Dihedral : 5.862 52.438 2743 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.33 % Allowed : 10.65 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.27), residues: 1017 helix: 0.59 (0.29), residues: 342 sheet: 0.68 (0.44), residues: 138 loop : 0.03 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG b 282 TYR 0.013 0.001 TYR A 66 PHE 0.008 0.001 PHE b 399 TRP 0.010 0.001 TRP A 210 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00277 (10505) covalent geometry : angle 0.51853 (14274) SS BOND : bond 0.00290 ( 21) SS BOND : angle 0.98499 ( 42) hydrogen bonds : bond 0.03349 ( 410) hydrogen bonds : angle 4.39193 ( 1107) link_ALPHA1-2 : bond 0.00966 ( 1) link_ALPHA1-2 : angle 1.69631 ( 3) link_ALPHA1-3 : bond 0.01020 ( 4) link_ALPHA1-3 : angle 1.23030 ( 12) link_ALPHA1-6 : bond 0.00669 ( 1) link_ALPHA1-6 : angle 1.48127 ( 3) link_BETA1-4 : bond 0.00335 ( 25) link_BETA1-4 : angle 1.81934 ( 75) link_BETA1-6 : bond 0.00268 ( 5) link_BETA1-6 : angle 1.34708 ( 15) link_NAG-ASN : bond 0.00190 ( 33) link_NAG-ASN : angle 2.08889 ( 99) *********************** 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 196 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7819 (mttt) REVERT: A 192 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8185 (ppp) REVERT: B 116 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8899 (mttm) REVERT: B 134 MET cc_start: 0.9219 (tpp) cc_final: 0.8725 (tpt) REVERT: C 95 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8671 (tt) REVERT: C 116 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8475 (mttm) REVERT: C 256 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.6799 (mtp85) REVERT: a 270 GLU cc_start: 0.5887 (mm-30) cc_final: 0.3487 (tm-30) REVERT: a 282 ARG cc_start: 0.8462 (ttp-110) cc_final: 0.7942 (ttp-170) REVERT: a 401 ASP cc_start: 0.8962 (m-30) cc_final: 0.8694 (m-30) REVERT: b 379 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7924 (ttp-110) REVERT: c 379 ARG cc_start: 0.8223 (ttm-80) cc_final: 0.7389 (ttp-110) outliers start: 31 outliers final: 19 residues processed: 179 average time/residue: 0.7221 time to fit residues: 137.2009 Evaluate side-chains 186 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 189 GLN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 232 GLN 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 95 ILE 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 341 VAL Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 388 VAL 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 53 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 41 optimal weight: 0.0370 chunk 76 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 b 321 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.143647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.125260 restraints weight = 11444.284| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.75 r_work: 0.3239 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10595 Z= 0.128 Angle : 0.577 8.353 14523 Z= 0.276 Chirality : 0.038 0.208 1833 Planarity : 0.003 0.043 1734 Dihedral : 5.784 51.261 2743 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.55 % Allowed : 10.43 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.27), residues: 1017 helix: 0.69 (0.29), residues: 339 sheet: 0.70 (0.44), residues: 138 loop : 0.05 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG b 282 TYR 0.013 0.001 TYR A 66 PHE 0.008 0.001 PHE b 399 TRP 0.010 0.001 TRP A 210 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00294 (10505) covalent geometry : angle 0.52919 (14274) SS BOND : bond 0.00462 ( 21) SS BOND : angle 1.46954 ( 42) hydrogen bonds : bond 0.03382 ( 410) hydrogen bonds : angle 4.37106 ( 1107) link_ALPHA1-2 : bond 0.00878 ( 1) link_ALPHA1-2 : angle 1.68563 ( 3) link_ALPHA1-3 : bond 0.00996 ( 4) link_ALPHA1-3 : angle 1.25160 ( 12) link_ALPHA1-6 : bond 0.00689 ( 1) link_ALPHA1-6 : angle 1.47104 ( 3) link_BETA1-4 : bond 0.00329 ( 25) link_BETA1-4 : angle 1.81755 ( 75) link_BETA1-6 : bond 0.00259 ( 5) link_BETA1-6 : angle 1.35893 ( 15) link_NAG-ASN : bond 0.00182 ( 33) link_NAG-ASN : angle 2.09088 ( 99) *********************** 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 195 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.7790 (mttt) REVERT: A 125 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8286 (tptp) REVERT: A 192 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8170 (ppp) REVERT: B 116 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8889 (mttm) REVERT: B 134 MET cc_start: 0.9207 (tpp) cc_final: 0.8711 (tpt) REVERT: C 95 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8635 (tt) REVERT: C 116 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8451 (mttm) REVERT: C 256 ARG cc_start: 0.8029 (mtm-85) cc_final: 0.6740 (mtp85) REVERT: a 270 GLU cc_start: 0.5850 (mm-30) cc_final: 0.3437 (tm-30) REVERT: a 282 ARG cc_start: 0.8461 (ttp-110) cc_final: 0.7927 (ttp-170) REVERT: a 332 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7184 (ttt) REVERT: b 379 ARG cc_start: 0.8225 (ttp80) cc_final: 0.7914 (ttp-110) REVERT: c 379 ARG cc_start: 0.8204 (ttm-80) cc_final: 0.7339 (ttp-110) outliers start: 33 outliers final: 21 residues processed: 177 average time/residue: 0.7281 time to fit residues: 136.6679 Evaluate side-chains 184 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 189 GLN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 232 GLN 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 95 ILE 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 341 VAL Chi-restraints excluded: chain a residue 367 SER Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 388 VAL 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 112 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 13 optimal weight: 0.0870 chunk 76 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.1364 ------------------------------------------------------------------------------- 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 b 321 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.141871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.123497 restraints weight = 11480.926| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.74 r_work: 0.3227 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10595 Z= 0.171 Angle : 0.648 14.704 14523 Z= 0.308 Chirality : 0.041 0.347 1833 Planarity : 0.003 0.044 1734 Dihedral : 6.077 53.440 2743 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.33 % Allowed : 10.86 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.27), residues: 1017 helix: 0.49 (0.28), residues: 342 sheet: 0.65 (0.45), residues: 138 loop : -0.02 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG b 282 TYR 0.015 0.002 TYR A 66 PHE 0.010 0.001 PHE b 399 TRP 0.008 0.001 TRP C 210 HIS 0.007 0.001 HIS C 179 Details of bonding type rmsd covalent geometry : bond 0.00400 (10505) covalent geometry : angle 0.59366 (14274) SS BOND : bond 0.00591 ( 21) SS BOND : angle 2.32293 ( 42) hydrogen bonds : bond 0.03718 ( 410) hydrogen bonds : angle 4.50245 ( 1107) link_ALPHA1-2 : bond 0.00778 ( 1) link_ALPHA1-2 : angle 1.82881 ( 3) link_ALPHA1-3 : bond 0.00948 ( 4) link_ALPHA1-3 : angle 1.30638 ( 12) link_ALPHA1-6 : bond 0.00558 ( 1) link_ALPHA1-6 : angle 1.51976 ( 3) link_BETA1-4 : bond 0.00327 ( 25) link_BETA1-4 : angle 1.97258 ( 75) link_BETA1-6 : bond 0.00232 ( 5) link_BETA1-6 : angle 1.44214 ( 15) link_NAG-ASN : bond 0.00265 ( 33) link_NAG-ASN : angle 2.20189 ( 99) *********************** 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 187 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.7817 (mttt) REVERT: A 125 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8330 (tptp) REVERT: A 192 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8265 (ppp) REVERT: B 116 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8858 (mttm) REVERT: C 95 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8653 (tp) REVERT: C 116 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8458 (mttm) REVERT: C 256 ARG cc_start: 0.8087 (mtm-85) cc_final: 0.6806 (mtp85) REVERT: a 270 GLU cc_start: 0.5921 (mm-30) cc_final: 0.3465 (tm-30) REVERT: a 282 ARG cc_start: 0.8508 (ttp-110) cc_final: 0.7970 (ttp-170) REVERT: a 401 ASP cc_start: 0.9047 (m-30) cc_final: 0.8820 (m-30) REVERT: b 379 ARG cc_start: 0.8246 (ttp80) cc_final: 0.7943 (ttp-110) REVERT: c 379 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.7350 (ttp-110) outliers start: 31 outliers final: 21 residues processed: 170 average time/residue: 0.7291 time to fit residues: 131.5736 Evaluate side-chains 184 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 189 GLN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 116 LYS 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 116 LYS Chi-restraints excluded: chain C residue 212 CYS 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 388 VAL 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 13 optimal weight: 0.1980 chunk 122 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 335 GLN b 321 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.142330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.124056 restraints weight = 11417.784| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.74 r_work: 0.3232 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10595 Z= 0.152 Angle : 0.624 14.107 14523 Z= 0.298 Chirality : 0.040 0.321 1833 Planarity : 0.003 0.043 1734 Dihedral : 5.972 52.953 2743 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.90 % Allowed : 10.97 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.27), residues: 1017 helix: 0.52 (0.28), residues: 342 sheet: 0.63 (0.44), residues: 138 loop : -0.06 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG b 282 TYR 0.014 0.001 TYR A 66 PHE 0.009 0.001 PHE b 399 TRP 0.011 0.001 TRP C 210 HIS 0.004 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00353 (10505) covalent geometry : angle 0.57127 (14274) SS BOND : bond 0.00469 ( 21) SS BOND : angle 2.19966 ( 42) hydrogen bonds : bond 0.03562 ( 410) hydrogen bonds : angle 4.46533 ( 1107) link_ALPHA1-2 : bond 0.00853 ( 1) link_ALPHA1-2 : angle 1.78629 ( 3) link_ALPHA1-3 : bond 0.00965 ( 4) link_ALPHA1-3 : angle 1.25232 ( 12) link_ALPHA1-6 : bond 0.00617 ( 1) link_ALPHA1-6 : angle 1.50764 ( 3) link_BETA1-4 : bond 0.00326 ( 25) link_BETA1-4 : angle 1.89752 ( 75) link_BETA1-6 : bond 0.00239 ( 5) link_BETA1-6 : angle 1.39337 ( 15) link_NAG-ASN : bond 0.00228 ( 33) link_NAG-ASN : angle 2.16402 ( 99) ********************** 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 184 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.7861 (mttt) REVERT: A 125 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8325 (tptp) REVERT: A 192 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8238 (ppp) REVERT: B 116 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8874 (mttm) REVERT: C 95 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8663 (tt) REVERT: C 256 ARG cc_start: 0.8081 (mtm-85) cc_final: 0.6793 (mtp85) REVERT: a 270 GLU cc_start: 0.5913 (mm-30) cc_final: 0.3468 (tm-30) REVERT: a 282 ARG cc_start: 0.8485 (ttp-110) cc_final: 0.7948 (ttp-170) REVERT: b 331 GLN cc_start: 0.7390 (tp-100) cc_final: 0.6078 (tt0) REVERT: b 379 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7960 (ttp-110) REVERT: c 379 ARG cc_start: 0.8223 (ttm-80) cc_final: 0.7353 (ttp-110) outliers start: 27 outliers final: 20 residues processed: 170 average time/residue: 0.7263 time to fit residues: 130.9156 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 : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 189 GLN Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 116 LYS 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 388 VAL 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 59 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 b 321 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.142133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.123771 restraints weight = 11534.528| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.75 r_work: 0.3230 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10595 Z= 0.153 Angle : 0.628 11.626 14523 Z= 0.299 Chirality : 0.040 0.315 1833 Planarity : 0.003 0.043 1734 Dihedral : 5.953 52.789 2743 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.01 % Allowed : 10.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.27), residues: 1017 helix: 0.51 (0.28), residues: 342 sheet: 0.65 (0.45), residues: 138 loop : -0.07 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG b 282 TYR 0.014 0.001 TYR A 66 PHE 0.010 0.001 PHE b 399 TRP 0.011 0.001 TRP C 210 HIS 0.004 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00357 (10505) covalent geometry : angle 0.57283 (14274) SS BOND : bond 0.00365 ( 21) SS BOND : angle 2.31630 ( 42) hydrogen bonds : bond 0.03595 ( 410) hydrogen bonds : angle 4.47129 ( 1107) link_ALPHA1-2 : bond 0.00840 ( 1) link_ALPHA1-2 : angle 1.79091 ( 3) link_ALPHA1-3 : bond 0.00920 ( 4) link_ALPHA1-3 : angle 1.26599 ( 12) link_ALPHA1-6 : bond 0.00615 ( 1) link_ALPHA1-6 : angle 1.51181 ( 3) link_BETA1-4 : bond 0.00321 ( 25) link_BETA1-4 : angle 1.91816 ( 75) link_BETA1-6 : bond 0.00251 ( 5) link_BETA1-6 : angle 1.40252 ( 15) link_NAG-ASN : bond 0.00236 ( 33) link_NAG-ASN : angle 2.17928 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3844.13 seconds wall clock time: 66 minutes 37.11 seconds (3997.11 seconds total)