Starting phenix.real_space_refine on Tue May 13 10:45:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tye_41715/05_2025/8tye_41715.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tye_41715/05_2025/8tye_41715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tye_41715/05_2025/8tye_41715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tye_41715/05_2025/8tye_41715.map" model { file = "/net/cci-nas-00/data/ceres_data/8tye_41715/05_2025/8tye_41715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tye_41715/05_2025/8tye_41715.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 6178 2.51 5 N 1630 2.21 5 O 2023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9921 Number of models: 1 Model: "" Number of chains: 33 Chain: "H" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 580 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'TRANS': 115} Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 116 Planarities with less than four sites: {'UNK:plan-1': 116} Unresolved non-hydrogen planarities: 116 Chain: "L" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 510 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'UNK:plan-1': 102} Unresolved non-hydrogen planarities: 102 Chain: "C" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1459 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 2 Chain: "A" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1459 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 2 Chain: "B" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1463 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain breaks: 2 Chain: "c" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1251 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "a" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1189 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 3, 'TRANS': 142} Chain breaks: 1 Chain: "b" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1189 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 3, 'TRANS': 142} Chain breaks: 1 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 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: "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: 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: "K" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 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: "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: 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "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: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.66, per 1000 atoms: 0.87 Number of scatterers: 9921 At special positions: 0 Unit cell: (104.4, 97.15, 103.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2023 8.00 N 1630 7.00 C 6178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=1.66 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=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.02 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.04 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 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=2.03 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 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 ALPHA1-6 " BMA E 3 " - " MAN E 4 " " BMA U 3 " - " MAN U 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " 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 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 S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " BETA1-6 " NAG D 1 " - " FUC D 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG F 1 " - " FUC F 3 " " NAG K 1 " - " FUC K 3 " NAG-ASN " NAG A 301 " - " ASN A 109 " " NAG A 302 " - " ASN A 89 " " NAG A 303 " - " ASN A 99 " " NAG B 301 " - " ASN B 89 " " NAG B 302 " - " ASN B 99 " " NAG B 303 " - " ASN B 119 " " NAG C 301 " - " ASN C 89 " " NAG C 302 " - " ASN C 99 " " NAG D 1 " - " ASN C 109 " " NAG E 1 " - " ASN C 79 " " NAG F 1 " - " ASN C 119 " " NAG G 1 " - " ASN C 167 " " NAG I 1 " - " ASN C 224 " " NAG J 1 " - " ASN A 79 " " NAG K 1 " - " ASN A 119 " " NAG M 1 " - " ASN A 167 " " NAG N 1 " - " ASN A 224 " " NAG O 1 " - " ASN B 79 " " NAG P 1 " - " ASN B 109 " " NAG Q 1 " - " ASN B 167 " " NAG R 1 " - " ASN B 224 " " NAG S 1 " - " ASN c 365 " " NAG T 1 " - " ASN c 373 " " NAG U 1 " - " ASN a 365 " " NAG V 1 " - " ASN a 373 " " NAG W 1 " - " ASN b 365 " " NAG X 1 " - " ASN b 373 " " NAG a 701 " - " ASN a 395 " " NAG a 702 " - " ASN a 390 " " NAG b 701 " - " ASN b 390 " " NAG b 702 " - " ASN b 395 " " NAG c 701 " - " ASN c 390 " " NAG c 702 " - " ASN c 395 " Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 988.7 milliseconds 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 14 sheets defined 39.1% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'H' and resid 69 through 73 Processing helix chain 'L' and resid 50 through 52 No H-bonds generated for 'chain 'L' and resid 50 through 52' Processing helix chain 'C' and resid 75 through 80 removed outlier: 4.345A pdb=" N MET C 80 " --> pdb=" O THR C 77 " (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 157 through 161 removed outlier: 3.987A pdb=" N LYS C 161 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 removed outlier: 4.054A pdb=" N GLY C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.949A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.793A pdb=" N THR A 77 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 4.414A 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 157 through 161 removed outlier: 3.867A pdb=" N GLY A 160 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 removed outlier: 4.049A pdb=" N GLY A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.669A pdb=" N LEU A 245 " --> pdb=" O TYR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 249 removed outlier: 4.476A pdb=" N THR A 249 " --> pdb=" O SER A 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'B' and resid 74 through 81 removed outlier: 4.042A pdb=" N THR B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N MET B 80 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.588A pdb=" N GLY B 160 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.943A pdb=" N GLY B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 246 removed outlier: 4.061A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'c' and resid 294 through 301 removed outlier: 3.802A pdb=" N LYS c 300 " --> pdb=" O THR c 296 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS c 301 " --> pdb=" O ALA c 297 " (cutoff:3.500A) Processing helix chain 'c' and resid 307 through 325 removed outlier: 3.674A pdb=" N ASP c 311 " --> pdb=" O GLU c 307 " (cutoff:3.500A) Processing helix chain 'c' and resid 334 through 345 removed outlier: 6.162A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.950A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 399 through 414 removed outlier: 3.590A pdb=" N ILE c 403 " --> pdb=" O PHE c 399 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR c 412 " --> pdb=" O ASP c 408 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU c 413 " --> pdb=" O ASN c 409 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET c 414 " --> pdb=" O MET c 410 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 302 removed outlier: 3.548A pdb=" N VAL a 298 " --> pdb=" O GLY a 294 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS a 301 " --> pdb=" O ALA a 297 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN a 302 " --> pdb=" O VAL a 298 " (cutoff:3.500A) Processing helix chain 'a' and resid 308 through 326 Processing helix chain 'a' and resid 334 through 339 Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.827A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 399 through 413 removed outlier: 4.039A pdb=" N GLU a 413 " --> pdb=" O ASN a 409 " (cutoff:3.500A) Processing helix chain 'b' and resid 294 through 304 removed outlier: 3.577A pdb=" N VAL b 298 " --> pdb=" O GLY b 294 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN b 302 " --> pdb=" O VAL b 298 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU b 303 " --> pdb=" O ALA b 299 " (cutoff:3.500A) Processing helix chain 'b' and resid 307 through 326 removed outlier: 3.822A pdb=" N GLN b 324 " --> pdb=" O LYS b 320 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU b 326 " --> pdb=" O ALA b 322 " (cutoff:3.500A) Processing helix chain 'b' and resid 334 through 340 removed outlier: 3.669A pdb=" N ALA b 340 " --> pdb=" O LEU b 336 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.533A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 396 through 398 No H-bonds generated for 'chain 'b' and resid 396 through 398' Processing helix chain 'b' and resid 399 through 414 removed outlier: 4.007A pdb=" N GLU b 413 " --> pdb=" O ASN b 409 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N MET b 414 " --> pdb=" O MET b 410 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 35A through 38 Processing sheet with id=AA2, first strand: chain 'H' and resid 65 through 68 Processing sheet with id=AA3, first strand: chain 'L' and resid 35 through 37 Processing sheet with id=AA4, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 62 removed outlier: 3.518A pdb=" N TYR C 66 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR c 371 " --> pdb=" O GLN C 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AA7, first strand: chain 'A' and resid 66 through 72 removed outlier: 4.008A pdb=" N ASN a 365 " --> pdb=" O TRP a 386 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N TRP a 386 " --> pdb=" O ASN a 365 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N SER a 367 " --> pdb=" O LYS a 384 " (cutoff:3.500A) removed outlier: 10.446A pdb=" N LYS a 384 " --> pdb=" O SER a 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 84 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AB1, first strand: chain 'B' and resid 84 through 87 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 'b' and resid 278 through 280 Processing sheet with id=AB5, first strand: chain 'b' and resid 388 through 389 removed outlier: 3.540A pdb=" N SER b 389 " --> pdb=" O SER b 392 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 873 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: 2.55 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3035 1.34 - 1.46: 2528 1.46 - 1.59: 4387 1.59 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 10088 Sorted by residual: bond pdb=" C SER C 237 " pdb=" N PRO C 238 " ideal model delta sigma weight residual 1.331 1.354 -0.023 7.90e-03 1.60e+04 8.27e+00 bond pdb=" N TRP a 264 " pdb=" CA TRP a 264 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.23e-02 6.61e+03 8.21e+00 bond pdb=" N ILE b 286 " pdb=" CA ILE b 286 " ideal model delta sigma weight residual 1.459 1.492 -0.034 1.19e-02 7.06e+03 8.01e+00 bond pdb=" N ILE b 337 " pdb=" CA ILE b 337 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 7.95e+00 bond pdb=" N PHE b 262 " pdb=" CA PHE b 262 " ideal model delta sigma weight residual 1.455 1.490 -0.036 1.27e-02 6.20e+03 7.85e+00 ... (remaining 10083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 12801 1.89 - 3.78: 728 3.78 - 5.67: 128 5.67 - 7.56: 30 7.56 - 9.45: 7 Bond angle restraints: 13694 Sorted by residual: angle pdb=" CB LYS A 63 " pdb=" CG LYS A 63 " pdb=" CD LYS A 63 " ideal model delta sigma weight residual 111.30 120.18 -8.88 2.30e+00 1.89e-01 1.49e+01 angle pdb=" CA CYS C 86 " pdb=" CB CYS C 86 " pdb=" SG CYS C 86 " ideal model delta sigma weight residual 114.40 122.70 -8.30 2.30e+00 1.89e-01 1.30e+01 angle pdb=" N ILE b 334 " pdb=" CA ILE b 334 " pdb=" C ILE b 334 " ideal model delta sigma weight residual 113.07 108.19 4.88 1.36e+00 5.41e-01 1.29e+01 angle pdb=" N ASN a 365 " pdb=" CA ASN a 365 " pdb=" C ASN a 365 " ideal model delta sigma weight residual 113.28 109.01 4.27 1.22e+00 6.72e-01 1.22e+01 angle pdb=" N ALA b 330 " pdb=" CA ALA b 330 " pdb=" C ALA b 330 " ideal model delta sigma weight residual 111.28 107.48 3.80 1.09e+00 8.42e-01 1.22e+01 ... (remaining 13689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.26: 6360 22.26 - 44.52: 337 44.52 - 66.78: 63 66.78 - 89.04: 43 89.04 - 111.30: 22 Dihedral angle restraints: 6825 sinusoidal: 3260 harmonic: 3565 Sorted by residual: dihedral pdb=" CB CYS a 364 " pdb=" SG CYS a 364 " pdb=" SG CYS a 385 " pdb=" CB CYS a 385 " ideal model delta sinusoidal sigma weight residual -86.00 -169.64 83.64 1 1.00e+01 1.00e-02 8.54e+01 dihedral pdb=" CB CYS B 207 " pdb=" SG CYS B 207 " pdb=" SG CYS b 360 " pdb=" CB CYS b 360 " ideal model delta sinusoidal sigma weight residual -86.00 -32.94 -53.06 1 1.00e+01 1.00e-02 3.83e+01 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 93.00 130.83 -37.83 1 1.00e+01 1.00e-02 2.02e+01 ... (remaining 6822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 1695 0.148 - 0.296: 42 0.296 - 0.444: 6 0.444 - 0.592: 1 0.592 - 0.741: 2 Chirality restraints: 1746 Sorted by residual: chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-02 2.50e+03 1.10e+03 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-02 2.50e+03 4.11e+02 chirality pdb=" C1 BMA U 3 " pdb=" O4 NAG U 2 " pdb=" C2 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.33e+02 ... (remaining 1743 not shown) Planarity restraints: 1697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 2 " -0.370 2.00e-02 2.50e+03 3.17e-01 1.25e+03 pdb=" C7 NAG T 2 " 0.091 2.00e-02 2.50e+03 pdb=" C8 NAG T 2 " -0.124 2.00e-02 2.50e+03 pdb=" N2 NAG T 2 " 0.562 2.00e-02 2.50e+03 pdb=" O7 NAG T 2 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.346 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG E 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.516 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.215 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG U 1 " 0.334 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG U 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG U 1 " 0.148 2.00e-02 2.50e+03 pdb=" N2 NAG U 1 " -0.512 2.00e-02 2.50e+03 pdb=" O7 NAG U 1 " 0.113 2.00e-02 2.50e+03 ... (remaining 1694 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 838 2.74 - 3.28: 10384 3.28 - 3.82: 15616 3.82 - 4.36: 18268 4.36 - 4.90: 31112 Nonbonded interactions: 76218 Sorted by model distance: nonbonded pdb=" OG1 THR C 81 " pdb=" OD1 ASN c 319 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP b 311 " pdb=" NH2 ARG b 314 " model vdw 2.247 3.120 nonbonded pdb=" NZ LYS A 116 " pdb=" O7 NAG M 1 " model vdw 2.248 3.120 nonbonded pdb=" N GLY a 277 " pdb=" OD1 ASN a 295 " model vdw 2.253 3.120 nonbonded pdb=" NH2 ARG C 256 " pdb=" OG SER A 255 " model vdw 2.256 3.120 ... (remaining 76213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 60 through 259 or resid 301 through 302)) selection = (chain 'B' and (resid 60 through 197 or resid 207 through 259 or resid 301 throu \ gh 302)) selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'X' and resid 1) } ncs_group { reference = chain 'E' selection = chain 'U' } ncs_group { reference = (chain 'F' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) } ncs_group { reference = (chain 'H' and resid 15 through 109) selection = chain 'L' } ncs_group { reference = chain 'a' selection = chain 'b' selection = (chain 'c' and (resid 260 through 267 or resid 277 through 414 or resid 701 thro \ ugh 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 6.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.880 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 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 : 0.007 0.371 10170 Z= 0.356 Angle : 1.116 33.157 13919 Z= 0.534 Chirality : 0.064 0.741 1746 Planarity : 0.025 0.317 1664 Dihedral : 16.149 111.296 4440 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.26), residues: 966 helix: -0.10 (0.27), residues: 309 sheet: -1.70 (0.40), residues: 158 loop : -0.92 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP a 386 HIS 0.014 0.002 HIS c 354 PHE 0.019 0.002 PHE a 318 TYR 0.025 0.002 TYR a 363 ARG 0.014 0.001 ARG B 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 33) link_NAG-ASN : angle 2.96456 ( 99) link_ALPHA1-6 : bond 0.00298 ( 2) link_ALPHA1-6 : angle 2.39482 ( 6) link_BETA1-4 : bond 0.00797 ( 23) link_BETA1-4 : angle 3.21603 ( 69) hydrogen bonds : bond 0.17996 ( 331) hydrogen bonds : angle 6.83614 ( 873) link_BETA1-6 : bond 0.00429 ( 3) link_BETA1-6 : angle 1.32919 ( 9) SS BOND : bond 0.08105 ( 21) SS BOND : angle 6.03196 ( 42) covalent geometry : bond 0.00597 (10088) covalent geometry : angle 1.01734 (13694) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 211 ASP cc_start: 0.8193 (t0) cc_final: 0.7895 (t0) REVERT: A 129 TYR cc_start: 0.7807 (p90) cc_final: 0.7553 (p90) REVERT: A 193 ARG cc_start: 0.8223 (mtp180) cc_final: 0.7683 (mtp180) REVERT: A 194 MET cc_start: 0.7239 (tpp) cc_final: 0.6654 (tpp) REVERT: B 76 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7995 (mp0) REVERT: B 151 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8142 (mm-30) REVERT: B 245 LEU cc_start: 0.9402 (mt) cc_final: 0.8993 (tt) REVERT: c 286 ILE cc_start: 0.8907 (pt) cc_final: 0.7969 (pt) REVERT: c 295 ASN cc_start: 0.8628 (t0) cc_final: 0.8226 (t0) REVERT: c 379 ARG cc_start: 0.8248 (mmp80) cc_final: 0.7884 (mmm160) REVERT: a 357 ASP cc_start: 0.8690 (t70) cc_final: 0.8330 (t0) REVERT: a 363 TYR cc_start: 0.7670 (p90) cc_final: 0.7463 (p90) REVERT: a 398 HIS cc_start: 0.7501 (m-70) cc_final: 0.7151 (m-70) REVERT: b 358 ILE cc_start: 0.9104 (tt) cc_final: 0.8876 (tt) REVERT: b 381 SER cc_start: 0.8877 (p) cc_final: 0.8624 (t) REVERT: b 400 SER cc_start: 0.8552 (p) cc_final: 0.8327 (m) REVERT: b 414 MET cc_start: 0.6937 (mpp) cc_final: 0.6639 (mpp) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.2551 time to fit residues: 108.2721 Evaluate side-chains 254 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 ASN A 209 ASN c 354 HIS c 409 ASN a 335 GLN a 374 HIS b 335 GLN b 409 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.126470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.105562 restraints weight = 21007.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.108948 restraints weight = 11561.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.111301 restraints weight = 7550.159| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10170 Z= 0.206 Angle : 0.885 9.749 13919 Z= 0.393 Chirality : 0.048 0.341 1746 Planarity : 0.004 0.038 1664 Dihedral : 11.967 83.148 2534 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.11 % Allowed : 11.21 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.27), residues: 966 helix: 0.37 (0.28), residues: 331 sheet: -1.57 (0.41), residues: 147 loop : -0.79 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 227 HIS 0.012 0.002 HIS B 93 PHE 0.023 0.002 PHE b 399 TYR 0.018 0.002 TYR B 241 ARG 0.009 0.001 ARG C 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 33) link_NAG-ASN : angle 2.51690 ( 99) link_ALPHA1-6 : bond 0.00838 ( 2) link_ALPHA1-6 : angle 3.24962 ( 6) link_BETA1-4 : bond 0.00937 ( 23) link_BETA1-4 : angle 2.75463 ( 69) hydrogen bonds : bond 0.04920 ( 331) hydrogen bonds : angle 5.55258 ( 873) link_BETA1-6 : bond 0.00462 ( 3) link_BETA1-6 : angle 1.46986 ( 9) SS BOND : bond 0.00441 ( 21) SS BOND : angle 1.44635 ( 42) covalent geometry : bond 0.00457 (10088) covalent geometry : angle 0.83669 (13694) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 267 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8952 (mmmm) cc_final: 0.8556 (mppt) REVERT: A 129 TYR cc_start: 0.8144 (p90) cc_final: 0.7806 (p90) REVERT: B 67 GLU cc_start: 0.8289 (tp30) cc_final: 0.8051 (tp30) REVERT: B 76 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7966 (mp0) REVERT: B 245 LEU cc_start: 0.9529 (mt) cc_final: 0.8955 (tt) REVERT: B 257 ARG cc_start: 0.8487 (mtm180) cc_final: 0.8236 (mtm-85) REVERT: c 284 MET cc_start: 0.8619 (mpp) cc_final: 0.7891 (mtm) REVERT: c 295 ASN cc_start: 0.8445 (t0) cc_final: 0.8217 (t0) REVERT: a 357 ASP cc_start: 0.8763 (t70) cc_final: 0.8496 (t0) REVERT: a 398 HIS cc_start: 0.7788 (m-70) cc_final: 0.7370 (m-70) REVERT: a 402 ASP cc_start: 0.8793 (t70) cc_final: 0.8578 (t70) REVERT: b 289 GLU cc_start: 0.8293 (mp0) cc_final: 0.8089 (mp0) REVERT: b 381 SER cc_start: 0.8965 (p) cc_final: 0.8430 (t) REVERT: b 400 SER cc_start: 0.8618 (p) cc_final: 0.8256 (m) outliers start: 19 outliers final: 13 residues processed: 275 average time/residue: 0.2351 time to fit residues: 87.4010 Evaluate side-chains 253 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 240 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 344 LEU Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain a residue 392 SER Chi-restraints excluded: chain a residue 399 PHE Chi-restraints excluded: chain b residue 321 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 115 optimal weight: 3.9990 chunk 91 optimal weight: 0.0970 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 HIS A 179 HIS ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 354 HIS c 409 ASN b 374 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.123932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.103453 restraints weight = 21485.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.106630 restraints weight = 11999.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.108942 restraints weight = 7961.737| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 10170 Z= 0.202 Angle : 0.824 10.193 13919 Z= 0.370 Chirality : 0.046 0.310 1746 Planarity : 0.004 0.041 1664 Dihedral : 10.438 80.125 2534 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.66 % Allowed : 15.21 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.27), residues: 966 helix: 0.45 (0.28), residues: 333 sheet: -1.50 (0.40), residues: 160 loop : -0.67 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 227 HIS 0.008 0.001 HIS B 93 PHE 0.016 0.002 PHE b 399 TYR 0.025 0.002 TYR B 253 ARG 0.009 0.001 ARG B 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 33) link_NAG-ASN : angle 2.46684 ( 99) link_ALPHA1-6 : bond 0.01080 ( 2) link_ALPHA1-6 : angle 2.00102 ( 6) link_BETA1-4 : bond 0.00908 ( 23) link_BETA1-4 : angle 2.59822 ( 69) hydrogen bonds : bond 0.04346 ( 331) hydrogen bonds : angle 5.32804 ( 873) link_BETA1-6 : bond 0.00452 ( 3) link_BETA1-6 : angle 1.48816 ( 9) SS BOND : bond 0.00823 ( 21) SS BOND : angle 1.75007 ( 42) covalent geometry : bond 0.00454 (10088) covalent geometry : angle 0.77416 (13694) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 251 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 TYR cc_start: 0.7836 (p90) cc_final: 0.7576 (p90) REVERT: C 250 ARG cc_start: 0.8643 (mmm-85) cc_final: 0.8324 (ttp-170) REVERT: C 254 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8746 (pp) REVERT: A 129 TYR cc_start: 0.8226 (p90) cc_final: 0.7941 (p90) REVERT: A 194 MET cc_start: 0.7168 (tpp) cc_final: 0.6689 (tpp) REVERT: B 67 GLU cc_start: 0.8311 (tp30) cc_final: 0.8105 (tp30) REVERT: B 76 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8018 (mp0) REVERT: B 245 LEU cc_start: 0.9520 (mt) cc_final: 0.8927 (tt) REVERT: B 257 ARG cc_start: 0.8487 (mtm180) cc_final: 0.8203 (mtm-85) REVERT: c 284 MET cc_start: 0.8647 (mpp) cc_final: 0.8157 (mtm) REVERT: c 295 ASN cc_start: 0.8452 (t0) cc_final: 0.8231 (t0) REVERT: a 398 HIS cc_start: 0.7842 (m-70) cc_final: 0.7385 (m-70) REVERT: a 402 ASP cc_start: 0.8816 (t70) cc_final: 0.8532 (t0) REVERT: b 400 SER cc_start: 0.8623 (p) cc_final: 0.8270 (m) outliers start: 33 outliers final: 23 residues processed: 268 average time/residue: 0.2378 time to fit residues: 86.0954 Evaluate side-chains 262 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 238 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 400 SER Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain a residue 399 PHE Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 380 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 324 GLN a 405 GLN b 321 GLN b 405 GLN b 406 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.120445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.099778 restraints weight = 21623.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.102847 restraints weight = 12144.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.105069 restraints weight = 8197.734| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 10170 Z= 0.302 Angle : 0.946 13.574 13919 Z= 0.426 Chirality : 0.050 0.344 1746 Planarity : 0.004 0.045 1664 Dihedral : 10.277 83.596 2534 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.66 % Allowed : 17.20 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.27), residues: 966 helix: 0.24 (0.28), residues: 332 sheet: -1.33 (0.40), residues: 162 loop : -1.01 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP C 227 HIS 0.009 0.002 HIS C 141 PHE 0.017 0.002 PHE b 399 TYR 0.024 0.002 TYR B 241 ARG 0.006 0.001 ARG B 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 33) link_NAG-ASN : angle 2.83277 ( 99) link_ALPHA1-6 : bond 0.01082 ( 2) link_ALPHA1-6 : angle 2.06426 ( 6) link_BETA1-4 : bond 0.00822 ( 23) link_BETA1-4 : angle 2.63278 ( 69) hydrogen bonds : bond 0.04714 ( 331) hydrogen bonds : angle 5.63482 ( 873) link_BETA1-6 : bond 0.00432 ( 3) link_BETA1-6 : angle 1.69159 ( 9) SS BOND : bond 0.00676 ( 21) SS BOND : angle 1.67154 ( 42) covalent geometry : bond 0.00674 (10088) covalent geometry : angle 0.89687 (13694) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 252 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 MET cc_start: 0.9369 (ppp) cc_final: 0.9080 (ppp) REVERT: C 250 ARG cc_start: 0.8637 (mmm-85) cc_final: 0.8374 (ttp-170) REVERT: A 76 GLU cc_start: 0.7997 (mp0) cc_final: 0.7716 (mp0) REVERT: A 129 TYR cc_start: 0.8299 (p90) cc_final: 0.7979 (p90) REVERT: A 241 TYR cc_start: 0.9182 (t80) cc_final: 0.8982 (t80) REVERT: B 76 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7963 (mp0) REVERT: B 88 LYS cc_start: 0.8594 (tmtt) cc_final: 0.8049 (tmtt) REVERT: B 245 LEU cc_start: 0.9503 (mt) cc_final: 0.9026 (tt) REVERT: c 284 MET cc_start: 0.8756 (mpp) cc_final: 0.8448 (mtm) REVERT: c 369 TYR cc_start: 0.8244 (m-10) cc_final: 0.8011 (m-10) REVERT: a 402 ASP cc_start: 0.8794 (t70) cc_final: 0.8556 (t0) REVERT: a 410 MET cc_start: 0.8745 (tpp) cc_final: 0.8402 (tpp) outliers start: 33 outliers final: 27 residues processed: 271 average time/residue: 0.2467 time to fit residues: 90.2368 Evaluate side-chains 269 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 400 SER Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain a residue 399 PHE Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 369 TYR Chi-restraints excluded: chain b residue 371 TYR Chi-restraints excluded: chain b residue 380 THR Chi-restraints excluded: chain b residue 412 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 86 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 374 HIS a 405 GLN a 409 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.124780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.104355 restraints weight = 20771.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.107609 restraints weight = 11400.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.109805 restraints weight = 7504.262| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10170 Z= 0.152 Angle : 0.824 16.029 13919 Z= 0.368 Chirality : 0.046 0.306 1746 Planarity : 0.004 0.043 1664 Dihedral : 9.402 80.501 2534 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.11 % Allowed : 19.76 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.27), residues: 966 helix: 0.50 (0.29), residues: 333 sheet: -1.35 (0.44), residues: 140 loop : -0.83 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 210 HIS 0.005 0.001 HIS C 141 PHE 0.015 0.002 PHE a 309 TYR 0.025 0.001 TYR B 253 ARG 0.007 0.001 ARG B 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 33) link_NAG-ASN : angle 2.26926 ( 99) link_ALPHA1-6 : bond 0.01400 ( 2) link_ALPHA1-6 : angle 2.01968 ( 6) link_BETA1-4 : bond 0.00876 ( 23) link_BETA1-4 : angle 2.48854 ( 69) hydrogen bonds : bond 0.03920 ( 331) hydrogen bonds : angle 5.27477 ( 873) link_BETA1-6 : bond 0.00436 ( 3) link_BETA1-6 : angle 1.54273 ( 9) SS BOND : bond 0.00481 ( 21) SS BOND : angle 2.06992 ( 42) covalent geometry : bond 0.00343 (10088) covalent geometry : angle 0.77828 (13694) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 258 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.7339 (tm-30) cc_final: 0.6829 (tm-30) REVERT: C 129 TYR cc_start: 0.7988 (p90) cc_final: 0.7685 (p90) REVERT: C 153 MET cc_start: 0.9297 (ppp) cc_final: 0.9076 (ppp) REVERT: C 250 ARG cc_start: 0.8538 (mmm-85) cc_final: 0.8272 (ttp-170) REVERT: A 76 GLU cc_start: 0.7937 (mp0) cc_final: 0.7627 (mp0) REVERT: A 129 TYR cc_start: 0.8186 (p90) cc_final: 0.7903 (p90) REVERT: B 76 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8099 (mp0) REVERT: B 245 LEU cc_start: 0.9466 (mt) cc_final: 0.8924 (tt) REVERT: c 284 MET cc_start: 0.8777 (mpp) cc_final: 0.8535 (mtm) REVERT: a 379 ARG cc_start: 0.7280 (ttp-170) cc_final: 0.7010 (ttp-170) REVERT: a 398 HIS cc_start: 0.7868 (m-70) cc_final: 0.7303 (m-70) REVERT: a 402 ASP cc_start: 0.8737 (t70) cc_final: 0.8511 (t0) REVERT: b 400 SER cc_start: 0.8611 (p) cc_final: 0.8249 (m) outliers start: 28 outliers final: 19 residues processed: 277 average time/residue: 0.2479 time to fit residues: 91.7729 Evaluate side-chains 258 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 239 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 400 SER Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain a residue 399 PHE Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 349 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 82 optimal weight: 0.0970 chunk 52 optimal weight: 5.9990 chunk 45 optimal weight: 0.0970 chunk 12 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 409 ASN a 405 GLN b 409 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.124612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.103912 restraints weight = 21423.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.107254 restraints weight = 11931.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.109601 restraints weight = 7799.685| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10170 Z= 0.163 Angle : 0.825 14.863 13919 Z= 0.369 Chirality : 0.045 0.305 1746 Planarity : 0.003 0.037 1664 Dihedral : 9.120 79.791 2534 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.11 % Allowed : 19.31 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.27), residues: 966 helix: 0.57 (0.29), residues: 333 sheet: -1.31 (0.43), residues: 144 loop : -0.80 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 227 HIS 0.005 0.001 HIS C 141 PHE 0.015 0.002 PHE A 233 TYR 0.020 0.002 TYR B 241 ARG 0.009 0.001 ARG C 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 33) link_NAG-ASN : angle 2.26674 ( 99) link_ALPHA1-6 : bond 0.01268 ( 2) link_ALPHA1-6 : angle 2.04632 ( 6) link_BETA1-4 : bond 0.00882 ( 23) link_BETA1-4 : angle 2.49764 ( 69) hydrogen bonds : bond 0.03869 ( 331) hydrogen bonds : angle 5.15365 ( 873) link_BETA1-6 : bond 0.00449 ( 3) link_BETA1-6 : angle 1.49575 ( 9) SS BOND : bond 0.00699 ( 21) SS BOND : angle 2.10953 ( 42) covalent geometry : bond 0.00370 (10088) covalent geometry : angle 0.77907 (13694) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 258 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6789 (tm-30) REVERT: C 129 TYR cc_start: 0.7960 (p90) cc_final: 0.7636 (p90) REVERT: C 153 MET cc_start: 0.9293 (ppp) cc_final: 0.9062 (ppp) REVERT: C 250 ARG cc_start: 0.8580 (mmm-85) cc_final: 0.8331 (ttp-170) REVERT: A 76 GLU cc_start: 0.7902 (mp0) cc_final: 0.7618 (mp0) REVERT: A 129 TYR cc_start: 0.8184 (p90) cc_final: 0.7891 (p90) REVERT: A 196 TRP cc_start: 0.7909 (OUTLIER) cc_final: 0.6926 (t60) REVERT: B 76 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8068 (mp0) REVERT: B 245 LEU cc_start: 0.9439 (mt) cc_final: 0.8946 (tt) REVERT: c 284 MET cc_start: 0.8816 (mpp) cc_final: 0.8541 (mtm) REVERT: c 348 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8375 (mm-40) REVERT: c 351 MET cc_start: 0.9119 (tpp) cc_final: 0.8794 (tpp) REVERT: c 379 ARG cc_start: 0.8111 (mmp80) cc_final: 0.7866 (mmm160) REVERT: a 321 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8470 (mm-40) REVERT: a 402 ASP cc_start: 0.8728 (t70) cc_final: 0.8505 (t0) REVERT: b 400 SER cc_start: 0.8603 (p) cc_final: 0.8251 (m) outliers start: 37 outliers final: 27 residues processed: 282 average time/residue: 0.2456 time to fit residues: 93.2785 Evaluate side-chains 271 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 243 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 400 SER Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain a residue 399 PHE Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 364 CYS Chi-restraints excluded: chain b residue 380 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 14 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 52 optimal weight: 0.0050 chunk 15 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 overall best weight: 2.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 HIS ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 295 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN a 409 ASN b 321 GLN b 409 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.120541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.099786 restraints weight = 21635.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.102949 restraints weight = 12075.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.105199 restraints weight = 7973.614| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 10170 Z= 0.288 Angle : 0.928 13.654 13919 Z= 0.420 Chirality : 0.049 0.321 1746 Planarity : 0.004 0.034 1664 Dihedral : 9.574 83.453 2534 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.00 % Allowed : 21.20 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.27), residues: 966 helix: 0.35 (0.28), residues: 331 sheet: -1.28 (0.44), residues: 144 loop : -1.04 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 227 HIS 0.009 0.002 HIS C 141 PHE 0.017 0.002 PHE a 309 TYR 0.034 0.002 TYR B 253 ARG 0.008 0.001 ARG C 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 33) link_NAG-ASN : angle 2.52925 ( 99) link_ALPHA1-6 : bond 0.01093 ( 2) link_ALPHA1-6 : angle 2.21992 ( 6) link_BETA1-4 : bond 0.00862 ( 23) link_BETA1-4 : angle 2.63506 ( 69) hydrogen bonds : bond 0.04373 ( 331) hydrogen bonds : angle 5.47897 ( 873) link_BETA1-6 : bond 0.00416 ( 3) link_BETA1-6 : angle 1.75724 ( 9) SS BOND : bond 0.00526 ( 21) SS BOND : angle 1.87349 ( 42) covalent geometry : bond 0.00648 (10088) covalent geometry : angle 0.88246 (13694) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 242 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: C 151 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8347 (mp0) REVERT: C 153 MET cc_start: 0.9317 (ppp) cc_final: 0.9020 (ppp) REVERT: C 193 ARG cc_start: 0.8192 (mtp180) cc_final: 0.7852 (mtp180) REVERT: A 76 GLU cc_start: 0.7957 (mp0) cc_final: 0.7643 (mp0) REVERT: A 129 TYR cc_start: 0.8345 (p90) cc_final: 0.8008 (p90) REVERT: A 196 TRP cc_start: 0.8099 (OUTLIER) cc_final: 0.7094 (t60) REVERT: A 241 TYR cc_start: 0.9177 (t80) cc_final: 0.8938 (t80) REVERT: B 76 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8015 (mp0) REVERT: B 88 LYS cc_start: 0.8667 (tmtt) cc_final: 0.8092 (tmtt) REVERT: B 245 LEU cc_start: 0.9416 (mt) cc_final: 0.8977 (tt) REVERT: c 284 MET cc_start: 0.8860 (mpp) cc_final: 0.8508 (mtm) REVERT: c 370 TRP cc_start: 0.9031 (p-90) cc_final: 0.8794 (p90) REVERT: a 321 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8299 (mm-40) REVERT: a 379 ARG cc_start: 0.7405 (ttp-170) cc_final: 0.6838 (ttp-170) REVERT: a 402 ASP cc_start: 0.8789 (t70) cc_final: 0.8561 (t0) REVERT: b 292 CYS cc_start: 0.6498 (m) cc_final: 0.6246 (m) outliers start: 36 outliers final: 24 residues processed: 262 average time/residue: 0.2516 time to fit residues: 87.9765 Evaluate side-chains 257 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 231 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 400 SER Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain a residue 399 PHE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 371 TYR Chi-restraints excluded: chain b residue 380 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 25 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN a 409 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.124205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.103938 restraints weight = 21088.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.107173 restraints weight = 11386.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.109494 restraints weight = 7466.363| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10170 Z= 0.157 Angle : 0.829 12.883 13919 Z= 0.373 Chirality : 0.046 0.292 1746 Planarity : 0.004 0.054 1664 Dihedral : 9.100 80.927 2534 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.22 % Allowed : 22.97 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.27), residues: 966 helix: 0.36 (0.29), residues: 331 sheet: -1.15 (0.44), residues: 144 loop : -0.89 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 227 HIS 0.012 0.001 HIS C 179 PHE 0.017 0.002 PHE A 233 TYR 0.030 0.001 TYR B 253 ARG 0.011 0.001 ARG C 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 33) link_NAG-ASN : angle 2.20127 ( 99) link_ALPHA1-6 : bond 0.01268 ( 2) link_ALPHA1-6 : angle 2.08693 ( 6) link_BETA1-4 : bond 0.00850 ( 23) link_BETA1-4 : angle 2.47121 ( 69) hydrogen bonds : bond 0.03860 ( 331) hydrogen bonds : angle 5.18784 ( 873) link_BETA1-6 : bond 0.00418 ( 3) link_BETA1-6 : angle 1.57737 ( 9) SS BOND : bond 0.00388 ( 21) SS BOND : angle 1.40924 ( 42) covalent geometry : bond 0.00359 (10088) covalent geometry : angle 0.78973 (13694) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 252 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6875 (tm-30) REVERT: C 129 TYR cc_start: 0.7957 (p90) cc_final: 0.7602 (p90) REVERT: C 153 MET cc_start: 0.9300 (ppp) cc_final: 0.9028 (ppp) REVERT: A 76 GLU cc_start: 0.7967 (mp0) cc_final: 0.7603 (mp0) REVERT: A 129 TYR cc_start: 0.8213 (p90) cc_final: 0.7889 (p90) REVERT: A 196 TRP cc_start: 0.7990 (OUTLIER) cc_final: 0.6972 (t60) REVERT: B 76 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8027 (mp0) REVERT: B 245 LEU cc_start: 0.9433 (mt) cc_final: 0.8973 (tt) REVERT: c 284 MET cc_start: 0.8851 (mpp) cc_final: 0.8571 (mtm) REVERT: c 348 GLN cc_start: 0.9157 (mm-40) cc_final: 0.8449 (mm-40) REVERT: a 320 LYS cc_start: 0.8473 (mttt) cc_final: 0.8273 (mttt) REVERT: a 379 ARG cc_start: 0.7323 (ttp-170) cc_final: 0.7065 (ttp-170) REVERT: a 402 ASP cc_start: 0.8725 (t70) cc_final: 0.8512 (t0) REVERT: b 292 CYS cc_start: 0.6444 (m) cc_final: 0.6224 (m) REVERT: b 400 SER cc_start: 0.8567 (p) cc_final: 0.8250 (m) outliers start: 29 outliers final: 21 residues processed: 272 average time/residue: 0.2390 time to fit residues: 87.2900 Evaluate side-chains 257 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 235 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain a residue 399 PHE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 380 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 73 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 HIS ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 295 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN a 409 ASN b 409 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.123735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.103277 restraints weight = 21517.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.106513 restraints weight = 11835.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.108783 restraints weight = 7805.418| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10170 Z= 0.173 Angle : 0.852 12.348 13919 Z= 0.387 Chirality : 0.046 0.370 1746 Planarity : 0.004 0.038 1664 Dihedral : 9.012 80.410 2534 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.22 % Allowed : 23.53 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.27), residues: 966 helix: 0.31 (0.29), residues: 331 sheet: -0.96 (0.45), residues: 140 loop : -0.86 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP c 370 HIS 0.005 0.001 HIS c 354 PHE 0.019 0.002 PHE c 399 TYR 0.014 0.001 TYR A 241 ARG 0.009 0.001 ARG C 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 33) link_NAG-ASN : angle 2.13334 ( 99) link_ALPHA1-6 : bond 0.01215 ( 2) link_ALPHA1-6 : angle 2.03432 ( 6) link_BETA1-4 : bond 0.00853 ( 23) link_BETA1-4 : angle 2.48070 ( 69) hydrogen bonds : bond 0.03964 ( 331) hydrogen bonds : angle 5.21160 ( 873) link_BETA1-6 : bond 0.00417 ( 3) link_BETA1-6 : angle 1.54554 ( 9) SS BOND : bond 0.00498 ( 21) SS BOND : angle 1.56657 ( 42) covalent geometry : bond 0.00397 (10088) covalent geometry : angle 0.81468 (13694) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 249 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: C 67 GLU cc_start: 0.7351 (tm-30) cc_final: 0.6817 (tm-30) REVERT: C 129 TYR cc_start: 0.7974 (p90) cc_final: 0.7613 (p90) REVERT: C 153 MET cc_start: 0.9285 (ppp) cc_final: 0.9013 (ppp) REVERT: C 250 ARG cc_start: 0.8501 (mmm-85) cc_final: 0.8208 (ttp-170) REVERT: A 76 GLU cc_start: 0.7915 (mp0) cc_final: 0.7570 (mp0) REVERT: A 129 TYR cc_start: 0.8221 (p90) cc_final: 0.7886 (p90) REVERT: A 196 TRP cc_start: 0.7984 (OUTLIER) cc_final: 0.6916 (t60) REVERT: B 210 TRP cc_start: 0.7786 (p90) cc_final: 0.7530 (p-90) REVERT: B 241 TYR cc_start: 0.8796 (t80) cc_final: 0.8361 (t80) REVERT: B 245 LEU cc_start: 0.9365 (mt) cc_final: 0.8947 (tt) REVERT: c 284 MET cc_start: 0.8830 (mpp) cc_final: 0.8507 (mtm) REVERT: c 348 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8401 (mm-40) REVERT: c 351 MET cc_start: 0.9208 (tpp) cc_final: 0.9001 (tpp) REVERT: a 320 LYS cc_start: 0.8450 (mttt) cc_final: 0.8186 (mttt) REVERT: a 348 GLN cc_start: 0.8941 (mm-40) cc_final: 0.8259 (mm-40) REVERT: a 402 ASP cc_start: 0.8748 (t70) cc_final: 0.8532 (t0) REVERT: b 292 CYS cc_start: 0.6421 (m) cc_final: 0.6202 (m) REVERT: b 368 LYS cc_start: 0.8508 (tttm) cc_final: 0.8222 (tttm) REVERT: b 400 SER cc_start: 0.8579 (p) cc_final: 0.8270 (m) outliers start: 29 outliers final: 21 residues processed: 267 average time/residue: 0.2454 time to fit residues: 87.6147 Evaluate side-chains 259 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain a residue 399 PHE Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 380 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 295 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 409 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.125024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.104588 restraints weight = 21067.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.107826 restraints weight = 11498.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.110121 restraints weight = 7572.032| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10170 Z= 0.158 Angle : 0.850 12.911 13919 Z= 0.387 Chirality : 0.046 0.312 1746 Planarity : 0.004 0.038 1664 Dihedral : 8.759 79.559 2534 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.35 % Favored : 95.55 % Rotamer: Outliers : 2.55 % Allowed : 23.97 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.27), residues: 966 helix: 0.26 (0.29), residues: 331 sheet: -0.84 (0.45), residues: 140 loop : -0.84 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 227 HIS 0.006 0.001 HIS C 179 PHE 0.018 0.002 PHE c 399 TYR 0.015 0.001 TYR A 241 ARG 0.009 0.001 ARG A 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 33) link_NAG-ASN : angle 2.08077 ( 99) link_ALPHA1-6 : bond 0.01198 ( 2) link_ALPHA1-6 : angle 1.99212 ( 6) link_BETA1-4 : bond 0.00852 ( 23) link_BETA1-4 : angle 2.43967 ( 69) hydrogen bonds : bond 0.03879 ( 331) hydrogen bonds : angle 5.18775 ( 873) link_BETA1-6 : bond 0.00421 ( 3) link_BETA1-6 : angle 1.48714 ( 9) SS BOND : bond 0.00484 ( 21) SS BOND : angle 1.42913 ( 42) covalent geometry : bond 0.00364 (10088) covalent geometry : angle 0.81505 (13694) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 245 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.7380 (tm-30) cc_final: 0.6836 (tm-30) REVERT: C 129 TYR cc_start: 0.7914 (p90) cc_final: 0.7561 (p90) REVERT: C 193 ARG cc_start: 0.8064 (mtp-110) cc_final: 0.7607 (ttp80) REVERT: C 250 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.8182 (ttp-170) REVERT: A 76 GLU cc_start: 0.7905 (mp0) cc_final: 0.7551 (mp0) REVERT: A 129 TYR cc_start: 0.8154 (p90) cc_final: 0.7846 (p90) REVERT: A 193 ARG cc_start: 0.8308 (mtp-110) cc_final: 0.8055 (mtp-110) REVERT: A 196 TRP cc_start: 0.7970 (OUTLIER) cc_final: 0.6866 (t60) REVERT: B 76 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8075 (mt-10) REVERT: B 210 TRP cc_start: 0.7767 (p90) cc_final: 0.7548 (p-90) REVERT: B 241 TYR cc_start: 0.8719 (t80) cc_final: 0.8420 (t80) REVERT: B 245 LEU cc_start: 0.9340 (mt) cc_final: 0.8961 (tt) REVERT: c 284 MET cc_start: 0.8816 (mpp) cc_final: 0.8549 (mtm) REVERT: a 402 ASP cc_start: 0.8738 (t70) cc_final: 0.8513 (t0) REVERT: b 292 CYS cc_start: 0.6435 (m) cc_final: 0.6214 (m) REVERT: b 368 LYS cc_start: 0.8429 (tttm) cc_final: 0.8146 (tttm) REVERT: b 400 SER cc_start: 0.8600 (p) cc_final: 0.8294 (m) outliers start: 23 outliers final: 20 residues processed: 258 average time/residue: 0.2382 time to fit residues: 81.7121 Evaluate side-chains 259 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 238 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain a residue 399 PHE Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 380 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 31 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 100 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 295 ASN a 319 ASN b 409 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.125401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.104719 restraints weight = 21286.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.107994 restraints weight = 11881.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.110353 restraints weight = 7792.364| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10170 Z= 0.155 Angle : 0.836 11.733 13919 Z= 0.381 Chirality : 0.045 0.305 1746 Planarity : 0.004 0.039 1664 Dihedral : 8.594 79.003 2534 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.76 % Favored : 95.13 % Rotamer: Outliers : 2.44 % Allowed : 23.86 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.27), residues: 966 helix: 0.36 (0.29), residues: 333 sheet: -0.76 (0.45), residues: 140 loop : -0.82 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP c 370 HIS 0.005 0.001 HIS c 354 PHE 0.015 0.002 PHE c 309 TYR 0.014 0.001 TYR A 241 ARG 0.009 0.001 ARG A 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 33) link_NAG-ASN : angle 2.04852 ( 99) link_ALPHA1-6 : bond 0.01171 ( 2) link_ALPHA1-6 : angle 1.93543 ( 6) link_BETA1-4 : bond 0.00866 ( 23) link_BETA1-4 : angle 2.42946 ( 69) hydrogen bonds : bond 0.03775 ( 331) hydrogen bonds : angle 5.12592 ( 873) link_BETA1-6 : bond 0.00425 ( 3) link_BETA1-6 : angle 1.43678 ( 9) SS BOND : bond 0.00370 ( 21) SS BOND : angle 1.34124 ( 42) covalent geometry : bond 0.00356 (10088) covalent geometry : angle 0.80115 (13694) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3336.45 seconds wall clock time: 59 minutes 51.32 seconds (3591.32 seconds total)