Starting phenix.real_space_refine on Thu Jul 2 19:50:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ejd_28178/07_2026/8ejd_28178.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejd_28178/07_2026/8ejd_28178.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 { model { file = "/net/cci-nas-00/data/ceres_data/8ejd_28178/07_2026/8ejd_28178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejd_28178/07_2026/8ejd_28178.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ejd_28178/07_2026/8ejd_28178.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ejd_28178/07_2026/8ejd_28178.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ejd_28178/07_2026/8ejd_28178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejd_28178/07_2026/8ejd_28178.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 93 5.16 5 C 6093 2.51 5 N 1524 2.21 5 O 2094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9804 Number of models: 1 Model: "" Number of chains: 36 Chain: "C" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1551 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "c" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1339 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "A" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1551 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "a" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1339 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "B" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1551 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "b" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1339 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "D" 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 chiralities: 3 Chain: "E" 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 chiralities: 3 Chain: "F" 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 chiralities: 2 Chain: "G" 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 chiralities: 3 Chain: "H" 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 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 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 chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "M" 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 chiralities: 3 Chain: "N" 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 chiralities: 3 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 chiralities: 2 Chain: "P" 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 chiralities: 3 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 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 chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 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 chiralities: 2 Chain: "Y" 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 chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "g" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 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 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 chiralities: 2 Time building chain proxies: 2.26, per 1000 atoms: 0.23 Number of scatterers: 9804 At special positions: 0 Unit cell: (100.05, 98.9, 102.35, 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 93 16.00 O 2094 8.00 N 1524 7.00 C 6093 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=2.02 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.02 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 c 279 " - pdb=" SG CYS c 292 " distance=2.04 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 86 " - pdb=" SG CYS A 231 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.03 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.04 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.02 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.02 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.02 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.03 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.04 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 ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA T 3 " - " MAN T 4 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 4 " " MAN L 4 " - " MAN L 5 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 5 " " BMA f 3 " - " MAN f 5 " " BMA g 3 " - " MAN g 4 " " MAN g 4 " - " MAN g 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " BETA1-6 " NAG G 1 " - " FUC G 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG P 1 " - " FUC P 3 " " NAG Y 1 " - " FUC Y 3 " NAG-ASN " NAG D 1 " - " ASN C 79 " " NAG E 1 " - " ASN C 89 " " NAG F 1 " - " ASN C 99 " " NAG G 1 " - " ASN C 109 " " NAG H 1 " - " ASN C 119 " " NAG I 1 " - " ASN C 167 " " NAG J 1 " - " ASN C 224 " " NAG K 1 " - " ASN c 365 " " NAG L 1 " - " ASN c 373 " " NAG M 1 " - " ASN A 79 " " NAG N 1 " - " ASN A 89 " " NAG O 1 " - " ASN A 99 " " NAG P 1 " - " ASN A 109 " " NAG Q 1 " - " ASN A 119 " " NAG R 1 " - " ASN A 167 " " NAG S 1 " - " ASN A 224 " " NAG T 1 " - " ASN a 365 " " NAG U 1 " - " ASN a 373 " " NAG V 1 " - " ASN B 79 " " NAG W 1 " - " ASN B 89 " " NAG X 1 " - " ASN B 99 " " NAG Y 1 " - " ASN B 109 " " NAG Z 1 " - " ASN B 119 " " NAG a 701 " - " ASN a 390 " " NAG a 702 " - " ASN a 395 " " NAG b 701 " - " ASN b 390 " " NAG b 702 " - " ASN b 395 " " NAG c 701 " - " ASN c 390 " " NAG c 702 " - " ASN c 395 " " NAG d 1 " - " ASN B 167 " " NAG e 1 " - " ASN B 224 " " NAG f 1 " - " ASN b 365 " " NAG g 1 " - " ASN b 373 " Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 315.7 milliseconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 9 sheets defined 44.8% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.618A pdb=" N THR C 77 " --> pdb=" O ASN C 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN C 79 " --> pdb=" O GLU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 169 through 172 Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 205 through 213 removed outlier: 4.876A pdb=" N TRP C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP C 211 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE C 213 " --> pdb=" O TRP C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 246 Processing helix chain 'c' and resid 281 through 285 Processing helix chain 'c' and resid 295 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 308 through 325 removed outlier: 3.814A pdb=" N MET c 312 " --> pdb=" O GLU c 308 " (cutoff:3.500A) Processing helix chain 'c' and resid 333 through 345 removed outlier: 4.067A pdb=" N LYS c 339 " --> pdb=" O GLN c 335 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 Processing helix chain 'c' and resid 395 through 398 Processing helix chain 'c' and resid 399 through 424 Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.619A pdb=" N THR A 77 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN A 79 " --> pdb=" O GLU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 169 through 172 Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 205 through 213 removed outlier: 4.876A pdb=" N TRP A 210 " --> pdb=" O CYS A 207 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP A 211 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 213 " --> pdb=" O TRP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'a' and resid 281 through 285 Processing helix chain 'a' and resid 295 through 299 Processing helix chain 'a' and resid 300 through 303 Processing helix chain 'a' and resid 308 through 325 removed outlier: 3.814A pdb=" N MET a 312 " --> pdb=" O GLU a 308 " (cutoff:3.500A) Processing helix chain 'a' and resid 333 through 345 removed outlier: 4.067A pdb=" N LYS a 339 " --> pdb=" O GLN a 335 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 359 Processing helix chain 'a' and resid 395 through 398 Processing helix chain 'a' and resid 399 through 424 Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.619A pdb=" N THR B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN B 79 " --> pdb=" O GLU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 169 through 172 Processing helix chain 'B' and resid 182 through 195 Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 205 through 213 removed outlier: 4.876A pdb=" N TRP B 210 " --> pdb=" O CYS B 207 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP B 211 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE B 213 " --> pdb=" O TRP B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'b' and resid 281 through 285 Processing helix chain 'b' and resid 295 through 299 Processing helix chain 'b' and resid 300 through 303 Processing helix chain 'b' and resid 308 through 325 removed outlier: 3.814A pdb=" N MET b 312 " --> pdb=" O GLU b 308 " (cutoff:3.500A) Processing helix chain 'b' and resid 333 through 345 removed outlier: 4.067A pdb=" N LYS b 339 " --> pdb=" O GLN b 335 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 Processing helix chain 'b' and resid 395 through 398 Processing helix chain 'b' and resid 399 through 424 Processing sheet with id=AA1, first strand: chain 'C' and resid 61 through 62 removed outlier: 9.425A pdb=" N TYR c 366 " --> pdb=" O VAL c 388 " (cutoff:3.500A) removed outlier: 10.868A pdb=" N VAL c 388 " --> pdb=" O TYR c 366 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LYS c 368 " --> pdb=" O TRP c 386 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER c 392 " --> pdb=" O SER c 389 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 84 through 87 removed outlier: 3.511A pdb=" N TYR C 219 " --> pdb=" O THR C 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 277 through 280 Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 62 removed outlier: 9.424A pdb=" N TYR a 366 " --> pdb=" O VAL a 388 " (cutoff:3.500A) removed outlier: 10.868A pdb=" N VAL a 388 " --> pdb=" O TYR a 366 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LYS a 368 " --> pdb=" O TRP a 386 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER a 392 " --> pdb=" O SER a 389 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 87 removed outlier: 3.511A pdb=" N TYR A 219 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 277 through 280 Processing sheet with id=AA7, first strand: chain 'B' and resid 61 through 62 removed outlier: 9.425A pdb=" N TYR b 366 " --> pdb=" O VAL b 388 " (cutoff:3.500A) removed outlier: 10.869A pdb=" N VAL b 388 " --> pdb=" O TYR b 366 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LYS b 368 " --> pdb=" O TRP b 386 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER b 392 " --> pdb=" O SER b 389 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 84 through 87 removed outlier: 3.511A pdb=" N TYR B 219 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 277 through 280 402 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.44 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 2298 1.33 - 1.46: 3219 1.46 - 1.60: 4329 1.60 - 1.74: 6 1.74 - 1.88: 144 Bond restraints: 9996 Sorted by residual: bond pdb=" CB HIS C 93 " pdb=" CG HIS C 93 " ideal model delta sigma weight residual 1.497 1.419 0.078 1.40e-02 5.10e+03 3.07e+01 bond pdb=" CB HIS A 93 " pdb=" CG HIS A 93 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 3.04e+01 bond pdb=" CB HIS B 93 " pdb=" CG HIS B 93 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 3.02e+01 bond pdb=" CB HIS a 374 " pdb=" CG HIS a 374 " ideal model delta sigma weight residual 1.497 1.428 0.069 1.40e-02 5.10e+03 2.40e+01 bond pdb=" CB HIS c 374 " pdb=" CG HIS c 374 " ideal model delta sigma weight residual 1.497 1.428 0.069 1.40e-02 5.10e+03 2.40e+01 ... (remaining 9991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 12460 3.16 - 6.33: 995 6.33 - 9.49: 60 9.49 - 12.66: 12 12.66 - 15.82: 9 Bond angle restraints: 13536 Sorted by residual: angle pdb=" N GLY A 198 " pdb=" CA GLY A 198 " pdb=" C GLY A 198 " ideal model delta sigma weight residual 115.42 128.53 -13.11 1.27e+00 6.20e-01 1.07e+02 angle pdb=" N GLY C 198 " pdb=" CA GLY C 198 " pdb=" C GLY C 198 " ideal model delta sigma weight residual 115.42 128.49 -13.07 1.27e+00 6.20e-01 1.06e+02 angle pdb=" N GLY B 198 " pdb=" CA GLY B 198 " pdb=" C GLY B 198 " ideal model delta sigma weight residual 115.42 128.49 -13.07 1.27e+00 6.20e-01 1.06e+02 angle pdb=" N ILE b 345 " pdb=" CA ILE b 345 " pdb=" C ILE b 345 " ideal model delta sigma weight residual 108.58 119.35 -10.77 1.44e+00 4.82e-01 5.60e+01 angle pdb=" N ILE c 345 " pdb=" CA ILE c 345 " pdb=" C ILE c 345 " ideal model delta sigma weight residual 108.58 119.34 -10.76 1.44e+00 4.82e-01 5.59e+01 ... (remaining 13531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.64: 5019 15.64 - 31.28: 216 31.28 - 46.93: 30 46.93 - 62.57: 33 62.57 - 78.21: 15 Dihedral angle restraints: 5313 sinusoidal: 2136 harmonic: 3177 Sorted by residual: dihedral pdb=" CB CYS A 207 " pdb=" SG CYS A 207 " pdb=" SG CYS a 360 " pdb=" CB CYS a 360 " ideal model delta sinusoidal sigma weight residual -86.00 -163.11 77.11 1 1.00e+01 1.00e-02 7.46e+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 -86.00 -163.10 77.10 1 1.00e+01 1.00e-02 7.46e+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 -163.09 77.09 1 1.00e+01 1.00e-02 7.46e+01 ... (remaining 5310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.309: 1608 0.309 - 0.618: 132 0.618 - 0.927: 0 0.927 - 1.236: 0 1.236 - 1.545: 3 Chirality restraints: 1743 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-02 2.50e+03 2.25e+02 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-02 2.50e+03 2.24e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-02 2.50e+03 2.24e+02 ... (remaining 1740 not shown) Planarity restraints: 1626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 701 " 0.314 2.00e-02 2.50e+03 2.68e-01 8.95e+02 pdb=" C7 NAG c 701 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG c 701 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG c 701 " -0.466 2.00e-02 2.50e+03 pdb=" O7 NAG c 701 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 701 " -0.314 2.00e-02 2.50e+03 2.67e-01 8.94e+02 pdb=" C7 NAG a 701 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG a 701 " -0.181 2.00e-02 2.50e+03 pdb=" N2 NAG a 701 " 0.466 2.00e-02 2.50e+03 pdb=" O7 NAG a 701 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 701 " 0.314 2.00e-02 2.50e+03 2.67e-01 8.93e+02 pdb=" C7 NAG b 701 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG b 701 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG b 701 " -0.466 2.00e-02 2.50e+03 pdb=" O7 NAG b 701 " 0.052 2.00e-02 2.50e+03 ... (remaining 1623 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 4092 2.90 - 3.40: 9482 3.40 - 3.90: 16636 3.90 - 4.40: 19107 4.40 - 4.90: 29701 Nonbonded interactions: 79018 Sorted by model distance: nonbonded pdb=" C4 NAG K 1 " pdb=" O6 NAG K 1 " model vdw 2.400 2.776 nonbonded pdb=" C4 NAG f 1 " pdb=" O6 NAG f 1 " model vdw 2.400 2.776 nonbonded pdb=" C4 NAG T 1 " pdb=" O6 NAG T 1 " model vdw 2.400 2.776 nonbonded pdb=" OD2 ASP c 401 " pdb=" NZ LYS a 272 " model vdw 2.409 3.120 nonbonded pdb=" OD2 ASP a 401 " pdb=" NZ LYS b 272 " model vdw 2.409 3.120 ... (remaining 79013 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1 through 2) selection = (chain 'E' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'X' selection = chain 'Z' selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'T' selection = chain 'U' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.680 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 : 0.022 0.111 10104 Z= 1.202 Angle : 1.929 15.821 13839 Z= 1.142 Chirality : 0.169 1.545 1743 Planarity : 0.019 0.268 1593 Dihedral : 10.668 78.208 3210 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.24), residues: 1074 helix: -0.57 (0.24), residues: 369 sheet: 1.12 (0.43), residues: 129 loop : 0.06 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG a 325 TYR 0.063 0.008 TYR b 363 PHE 0.024 0.005 PHE B 233 TRP 0.039 0.008 TRP A 227 HIS 0.010 0.003 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.02164 / 1.17 ( 9996) covalent geometry : angle 1.83171 / 1.13 (13536) SS BOND : bond 0.00782 / 0.51 ( 21) SS BOND : angle 2.68900 / 1.58 ( 42) hydrogen bonds : bond 0.17915 / 11.79 ( 402) hydrogen bonds : angle 6.44707 / 4.51 ( 1044) link_ALPHA1-3 : bond 0.00336 / 0.16 ( 3) link_ALPHA1-3 : angle 1.09254 / 0.52 ( 9) link_ALPHA1-6 : bond 0.05644 / 3.68 ( 9) link_ALPHA1-6 : angle 3.27341 / 2.03 ( 27) link_BETA1-4 : bond 0.07019 / 4.20 ( 39) link_BETA1-4 : angle 5.91989 / 3.83 ( 117) link_BETA1-6 : bond 0.06036 / 2.79 ( 3) link_BETA1-6 : angle 3.01618 / 1.74 ( 9) link_NAG-ASN : bond 0.07145 / 4.59 ( 33) link_NAG-ASN : angle 3.63699 / 2.53 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 TYR cc_start: 0.7515 (m-80) cc_final: 0.7289 (m-80) REVERT: C 130 ASP cc_start: 0.8657 (t0) cc_final: 0.8383 (t0) REVERT: C 189 GLN cc_start: 0.8861 (mt0) cc_final: 0.8454 (mt0) REVERT: C 245 LEU cc_start: 0.8755 (mt) cc_final: 0.8540 (tt) REVERT: c 348 GLN cc_start: 0.8847 (mp10) cc_final: 0.8031 (mp10) REVERT: A 130 ASP cc_start: 0.8492 (t0) cc_final: 0.8286 (t0) REVERT: A 189 GLN cc_start: 0.8888 (mt0) cc_final: 0.8530 (mt0) REVERT: A 194 MET cc_start: 0.8774 (tpp) cc_final: 0.8470 (tpp) REVERT: A 245 LEU cc_start: 0.8868 (mt) cc_final: 0.8610 (tt) REVERT: a 321 GLN cc_start: 0.9343 (mm-40) cc_final: 0.9071 (mm-40) REVERT: a 348 GLN cc_start: 0.8765 (mp10) cc_final: 0.7962 (mp10) REVERT: a 405 GLN cc_start: 0.9028 (tp40) cc_final: 0.8795 (tp-100) REVERT: B 130 ASP cc_start: 0.8695 (t0) cc_final: 0.8334 (t70) REVERT: B 189 GLN cc_start: 0.9038 (mt0) cc_final: 0.8683 (mt0) REVERT: B 244 LEU cc_start: 0.9198 (mt) cc_final: 0.8500 (mt) REVERT: B 245 LEU cc_start: 0.8853 (mt) cc_final: 0.8563 (tt) REVERT: b 405 GLN cc_start: 0.8976 (tp40) cc_final: 0.8616 (tp-100) REVERT: b 409 ASN cc_start: 0.8998 (m-40) cc_final: 0.8636 (m110) REVERT: b 418 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8898 (tt0) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.1273 time to fit residues: 60.5631 Evaluate side-chains 204 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 93 HIS ** C 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 HIS A 170 HIS ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 324 GLN ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 416 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.097285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.076231 restraints weight = 25748.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.079209 restraints weight = 14325.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.081268 restraints weight = 10101.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.082716 restraints weight = 8096.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.083696 restraints weight = 6937.240| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10104 Z= 0.204 Angle : 1.048 12.951 13839 Z= 0.496 Chirality : 0.054 0.365 1743 Planarity : 0.005 0.033 1593 Dihedral : 5.690 32.219 1167 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.48 % Allowed : 10.56 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.25), residues: 1074 helix: 0.15 (0.25), residues: 390 sheet: 0.98 (0.44), residues: 126 loop : -0.27 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 235 TYR 0.025 0.003 TYR A 62 PHE 0.013 0.002 PHE A 233 TRP 0.010 0.002 TRP c 386 HIS 0.007 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 ( 9996) covalent geometry : angle 0.92514 / 0.47 (13536) SS BOND : bond 0.00611 / 0.34 ( 21) SS BOND : angle 2.32140 / 1.31 ( 42) hydrogen bonds : bond 0.05974 / 3.95 ( 402) hydrogen bonds : angle 5.06356 / 3.54 ( 1044) link_ALPHA1-3 : bond 0.00568 / 0.26 ( 3) link_ALPHA1-3 : angle 1.17115 / 0.58 ( 9) link_ALPHA1-6 : bond 0.00642 / 0.38 ( 9) link_ALPHA1-6 : angle 1.80682 / 1.24 ( 27) link_BETA1-4 : bond 0.01075 / 0.61 ( 39) link_BETA1-4 : angle 4.29007 / 2.75 ( 117) link_BETA1-6 : bond 0.00113 / 0.05 ( 3) link_BETA1-6 : angle 1.50530 / 0.87 ( 9) link_NAG-ASN : bond 0.00763 / 0.49 ( 33) link_NAG-ASN : angle 3.34330 / 2.25 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 245 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 TYR cc_start: 0.6963 (m-80) cc_final: 0.6377 (m-80) REVERT: C 80 MET cc_start: 0.9225 (mmt) cc_final: 0.8829 (tpp) REVERT: C 116 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8000 (mmtt) REVERT: C 130 ASP cc_start: 0.8407 (t0) cc_final: 0.7906 (t0) REVERT: C 189 GLN cc_start: 0.8710 (mt0) cc_final: 0.8471 (mt0) REVERT: C 194 MET cc_start: 0.9069 (tpt) cc_final: 0.8770 (tpt) REVERT: c 321 GLN cc_start: 0.9242 (mm110) cc_final: 0.8829 (mm-40) REVERT: c 332 MET cc_start: 0.7867 (tpp) cc_final: 0.7648 (mmm) REVERT: c 351 MET cc_start: 0.9190 (mmm) cc_final: 0.8931 (mmm) REVERT: c 409 ASN cc_start: 0.9362 (m-40) cc_final: 0.8928 (m-40) REVERT: c 410 MET cc_start: 0.7770 (ttm) cc_final: 0.7203 (ttm) REVERT: c 413 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7868 (tm-30) REVERT: c 417 LYS cc_start: 0.8670 (ptmm) cc_final: 0.8142 (pttp) REVERT: A 116 LYS cc_start: 0.8466 (mmtm) cc_final: 0.7632 (mmmt) REVERT: A 130 ASP cc_start: 0.8014 (t0) cc_final: 0.7757 (t0) REVERT: A 153 MET cc_start: 0.8251 (tmm) cc_final: 0.7616 (tmm) REVERT: A 194 MET cc_start: 0.9182 (tpp) cc_final: 0.8831 (tpt) REVERT: A 210 TRP cc_start: 0.7632 (t-100) cc_final: 0.7293 (t-100) REVERT: A 227 TRP cc_start: 0.8506 (t60) cc_final: 0.8126 (t60) REVERT: A 235 ARG cc_start: 0.8126 (ttm-80) cc_final: 0.7901 (ttm-80) REVERT: a 321 GLN cc_start: 0.9313 (mm-40) cc_final: 0.8754 (mm-40) REVERT: a 324 GLN cc_start: 0.8262 (tm130) cc_final: 0.7932 (tm-30) REVERT: a 374 HIS cc_start: 0.8196 (t-90) cc_final: 0.7701 (t70) REVERT: a 401 ASP cc_start: 0.7953 (p0) cc_final: 0.7733 (p0) REVERT: a 405 GLN cc_start: 0.9477 (tp40) cc_final: 0.9023 (tp-100) REVERT: a 409 ASN cc_start: 0.9178 (m-40) cc_final: 0.8858 (m-40) REVERT: a 410 MET cc_start: 0.7943 (ttm) cc_final: 0.7292 (ttm) REVERT: a 413 GLU cc_start: 0.8447 (tm-30) cc_final: 0.7989 (tm-30) REVERT: B 66 TYR cc_start: 0.6724 (m-80) cc_final: 0.5873 (m-10) REVERT: B 116 LYS cc_start: 0.8473 (mmtt) cc_final: 0.7714 (mmmt) REVERT: B 130 ASP cc_start: 0.8251 (t0) cc_final: 0.7765 (t0) REVERT: B 134 MET cc_start: 0.8684 (tpt) cc_final: 0.8473 (tpt) REVERT: B 189 GLN cc_start: 0.8757 (mt0) cc_final: 0.8448 (mt0) REVERT: B 210 TRP cc_start: 0.7827 (t-100) cc_final: 0.7377 (t-100) REVERT: b 332 MET cc_start: 0.7793 (tpp) cc_final: 0.7574 (tpt) REVERT: b 374 HIS cc_start: 0.8318 (t-90) cc_final: 0.7853 (t-90) REVERT: b 405 GLN cc_start: 0.9466 (tp40) cc_final: 0.9194 (tp-100) REVERT: b 410 MET cc_start: 0.7801 (ttm) cc_final: 0.6786 (ttt) REVERT: b 413 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7377 (tm-30) REVERT: b 417 LYS cc_start: 0.8623 (ptmm) cc_final: 0.8057 (pttt) outliers start: 24 outliers final: 14 residues processed: 258 average time/residue: 0.1085 time to fit residues: 38.3807 Evaluate side-chains 207 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 193 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain c residue 349 LEU Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain b residue 270 GLU Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 402 ASP Chi-restraints excluded: chain b residue 421 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 67 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 42 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 93 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 209 ASN ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN B 141 HIS B 209 ASN b 324 GLN ** b 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.095258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.074233 restraints weight = 26506.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.077115 restraints weight = 14969.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.079138 restraints weight = 10645.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.080614 restraints weight = 8527.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.081507 restraints weight = 7313.698| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10104 Z= 0.189 Angle : 0.933 11.208 13839 Z= 0.441 Chirality : 0.049 0.310 1743 Planarity : 0.004 0.039 1593 Dihedral : 5.670 33.619 1167 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.87 % Favored : 93.85 % Rotamer: Outliers : 2.59 % Allowed : 12.32 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.25), residues: 1074 helix: 0.28 (0.25), residues: 411 sheet: 0.75 (0.45), residues: 126 loop : -0.44 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 325 TYR 0.022 0.002 TYR b 371 PHE 0.029 0.002 PHE A 233 TRP 0.012 0.001 TRP c 386 HIS 0.007 0.001 HIS B 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 ( 9996) covalent geometry : angle 0.83661 / 0.42 (13536) SS BOND : bond 0.00425 / 0.24 ( 21) SS BOND : angle 2.52745 / 1.52 ( 42) hydrogen bonds : bond 0.04940 / 3.29 ( 402) hydrogen bonds : angle 4.59892 / 3.23 ( 1044) link_ALPHA1-3 : bond 0.00544 / 0.25 ( 3) link_ALPHA1-3 : angle 1.30299 / 0.65 ( 9) link_ALPHA1-6 : bond 0.00568 / 0.37 ( 9) link_ALPHA1-6 : angle 1.50258 / 0.97 ( 27) link_BETA1-4 : bond 0.00967 / 0.56 ( 39) link_BETA1-4 : angle 3.44258 / 2.20 ( 117) link_BETA1-6 : bond 0.00314 / 0.14 ( 3) link_BETA1-6 : angle 1.67919 / 0.98 ( 9) link_NAG-ASN : bond 0.00394 / 0.26 ( 33) link_NAG-ASN : angle 2.85837 / 1.90 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 219 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 TYR cc_start: 0.6436 (m-10) cc_final: 0.5872 (m-10) REVERT: C 80 MET cc_start: 0.9225 (mmt) cc_final: 0.8763 (tpp) REVERT: C 116 LYS cc_start: 0.8586 (mmtt) cc_final: 0.7688 (mmmt) REVERT: C 130 ASP cc_start: 0.8217 (t0) cc_final: 0.7736 (t0) REVERT: C 153 MET cc_start: 0.8543 (tmm) cc_final: 0.7937 (tmm) REVERT: C 194 MET cc_start: 0.9126 (tpt) cc_final: 0.8754 (tpt) REVERT: c 409 ASN cc_start: 0.9385 (m-40) cc_final: 0.8830 (m110) REVERT: c 410 MET cc_start: 0.7688 (ttm) cc_final: 0.6726 (ttt) REVERT: c 413 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8260 (tm-30) REVERT: c 418 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8703 (tm-30) REVERT: A 116 LYS cc_start: 0.8528 (mmtm) cc_final: 0.8253 (mmtt) REVERT: A 130 ASP cc_start: 0.8276 (t0) cc_final: 0.8052 (t0) REVERT: A 153 MET cc_start: 0.8464 (tmm) cc_final: 0.7699 (tmm) REVERT: A 189 GLN cc_start: 0.8776 (mt0) cc_final: 0.8421 (mm-40) REVERT: A 227 TRP cc_start: 0.8428 (t60) cc_final: 0.7933 (t60) REVERT: a 287 GLU cc_start: 0.7607 (tp30) cc_final: 0.7287 (tp30) REVERT: a 321 GLN cc_start: 0.9328 (mm-40) cc_final: 0.9092 (mm110) REVERT: a 324 GLN cc_start: 0.8243 (tm130) cc_final: 0.7617 (tm-30) REVERT: a 341 VAL cc_start: 0.9428 (t) cc_final: 0.9215 (t) REVERT: a 374 HIS cc_start: 0.8559 (t-90) cc_final: 0.8181 (t-90) REVERT: a 405 GLN cc_start: 0.9562 (tp40) cc_final: 0.9042 (tp-100) REVERT: a 409 ASN cc_start: 0.9345 (m-40) cc_final: 0.8938 (m-40) REVERT: a 413 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8216 (tm-30) REVERT: B 62 TYR cc_start: 0.6905 (m-80) cc_final: 0.6524 (m-80) REVERT: B 75 MET cc_start: 0.7662 (mtm) cc_final: 0.7432 (mtm) REVERT: B 116 LYS cc_start: 0.8393 (mmtt) cc_final: 0.7461 (mmmt) REVERT: B 130 ASP cc_start: 0.8256 (t0) cc_final: 0.7701 (t0) REVERT: B 134 MET cc_start: 0.8744 (tpt) cc_final: 0.8328 (tmm) REVERT: B 189 GLN cc_start: 0.8783 (mt0) cc_final: 0.7929 (mt0) REVERT: B 210 TRP cc_start: 0.7683 (t-100) cc_final: 0.6617 (t-100) REVERT: b 303 GLU cc_start: 0.8008 (tp30) cc_final: 0.7651 (tp30) REVERT: b 357 ASP cc_start: 0.8896 (t70) cc_final: 0.8683 (t0) REVERT: b 374 HIS cc_start: 0.8410 (t-90) cc_final: 0.8096 (t-90) REVERT: b 405 GLN cc_start: 0.9522 (tp40) cc_final: 0.9300 (tp-100) REVERT: b 414 MET cc_start: 0.8145 (tmm) cc_final: 0.7726 (ttm) REVERT: b 418 GLU cc_start: 0.9191 (tt0) cc_final: 0.8699 (mt-10) outliers start: 25 outliers final: 13 residues processed: 230 average time/residue: 0.0988 time to fit residues: 32.2156 Evaluate side-chains 202 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain c residue 349 LEU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain b residue 270 GLU Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 55 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 416 GLN B 90 ASN B 115 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.094452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.073484 restraints weight = 26912.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.076360 restraints weight = 15311.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.078343 restraints weight = 10881.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.079758 restraints weight = 8724.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.080698 restraints weight = 7503.575| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10104 Z= 0.174 Angle : 0.900 12.873 13839 Z= 0.420 Chirality : 0.049 0.344 1743 Planarity : 0.004 0.044 1593 Dihedral : 5.547 33.847 1167 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.90 % Allowed : 13.25 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.26), residues: 1074 helix: 0.41 (0.26), residues: 411 sheet: 0.63 (0.45), residues: 126 loop : -0.45 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 235 TYR 0.019 0.002 TYR A 62 PHE 0.023 0.002 PHE A 233 TRP 0.017 0.001 TRP C 210 HIS 0.005 0.001 HIS C 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 9996) covalent geometry : angle 0.80075 / 0.39 (13536) SS BOND : bond 0.00363 / 0.20 ( 21) SS BOND : angle 3.46046 / 2.02 ( 42) hydrogen bonds : bond 0.04529 / 3.00 ( 402) hydrogen bonds : angle 4.35605 / 3.06 ( 1044) link_ALPHA1-3 : bond 0.00556 / 0.26 ( 3) link_ALPHA1-3 : angle 1.29011 / 0.66 ( 9) link_ALPHA1-6 : bond 0.00479 / 0.30 ( 9) link_ALPHA1-6 : angle 1.57001 / 1.01 ( 27) link_BETA1-4 : bond 0.00802 / 0.45 ( 39) link_BETA1-4 : angle 3.15092 / 2.02 ( 117) link_BETA1-6 : bond 0.00195 / 0.09 ( 3) link_BETA1-6 : angle 1.62285 / 0.92 ( 9) link_NAG-ASN : bond 0.00351 / 0.23 ( 33) link_NAG-ASN : angle 2.75308 / 1.84 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 TYR cc_start: 0.6320 (m-10) cc_final: 0.5693 (m-10) REVERT: C 116 LYS cc_start: 0.8563 (mmtt) cc_final: 0.7674 (mmmt) REVERT: C 130 ASP cc_start: 0.8284 (t0) cc_final: 0.7715 (t0) REVERT: C 153 MET cc_start: 0.8556 (tmm) cc_final: 0.7954 (tmm) REVERT: c 410 MET cc_start: 0.7740 (ttm) cc_final: 0.6457 (ttt) REVERT: c 413 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8303 (tm-30) REVERT: c 418 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8923 (mt-10) REVERT: A 66 TYR cc_start: 0.6682 (m-80) cc_final: 0.5856 (m-10) REVERT: A 116 LYS cc_start: 0.8523 (mmtm) cc_final: 0.8174 (mmtt) REVERT: A 130 ASP cc_start: 0.8115 (t0) cc_final: 0.7799 (t0) REVERT: A 153 MET cc_start: 0.8551 (tmm) cc_final: 0.7734 (tmm) REVERT: A 189 GLN cc_start: 0.8741 (mt0) cc_final: 0.8222 (mm-40) REVERT: A 211 ASP cc_start: 0.8919 (m-30) cc_final: 0.8696 (m-30) REVERT: A 235 ARG cc_start: 0.8458 (ttm-80) cc_final: 0.8204 (ttm-80) REVERT: a 321 GLN cc_start: 0.9345 (mm-40) cc_final: 0.9064 (mm110) REVERT: a 324 GLN cc_start: 0.8313 (tm130) cc_final: 0.7640 (tm-30) REVERT: a 374 HIS cc_start: 0.8416 (t-90) cc_final: 0.8047 (t-90) REVERT: a 405 GLN cc_start: 0.9560 (tp40) cc_final: 0.9192 (tp-100) REVERT: a 409 ASN cc_start: 0.9360 (m-40) cc_final: 0.9009 (m110) REVERT: a 410 MET cc_start: 0.8113 (ttm) cc_final: 0.7242 (ttt) REVERT: a 413 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8226 (tm-30) REVERT: B 62 TYR cc_start: 0.6892 (m-80) cc_final: 0.6571 (m-80) REVERT: B 66 TYR cc_start: 0.6716 (m-80) cc_final: 0.6006 (m-10) REVERT: B 75 MET cc_start: 0.7750 (mtm) cc_final: 0.7497 (mtm) REVERT: B 116 LYS cc_start: 0.8321 (mmtt) cc_final: 0.7306 (mmmt) REVERT: B 125 LYS cc_start: 0.9000 (mmtm) cc_final: 0.8763 (mmtm) REVERT: B 130 ASP cc_start: 0.8339 (t0) cc_final: 0.7847 (t0) REVERT: B 189 GLN cc_start: 0.8780 (mt0) cc_final: 0.8544 (mt0) REVERT: B 210 TRP cc_start: 0.7566 (t-100) cc_final: 0.7092 (t-100) REVERT: b 303 GLU cc_start: 0.7929 (tp30) cc_final: 0.7555 (tp30) REVERT: b 374 HIS cc_start: 0.8439 (t-90) cc_final: 0.8060 (t-90) REVERT: b 405 GLN cc_start: 0.9528 (tp40) cc_final: 0.9312 (tp-100) REVERT: b 410 MET cc_start: 0.7981 (ttm) cc_final: 0.6811 (ttt) REVERT: b 413 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8063 (tm-30) REVERT: b 418 GLU cc_start: 0.9189 (tt0) cc_final: 0.8922 (tm-30) outliers start: 28 outliers final: 15 residues processed: 215 average time/residue: 0.1015 time to fit residues: 30.8164 Evaluate side-chains 196 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 349 LEU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain b residue 270 GLU Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 65 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 90 ASN C 115 HIS ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 416 GLN A 90 ASN a 416 GLN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 335 GLN b 416 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.093089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.071936 restraints weight = 27240.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.074744 restraints weight = 15671.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.076716 restraints weight = 11209.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.078110 restraints weight = 9031.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.079010 restraints weight = 7795.554| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10104 Z= 0.205 Angle : 0.881 10.921 13839 Z= 0.411 Chirality : 0.048 0.299 1743 Planarity : 0.004 0.064 1593 Dihedral : 5.447 32.011 1167 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.62 % Allowed : 14.91 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.26), residues: 1074 helix: 0.87 (0.27), residues: 387 sheet: 0.68 (0.54), residues: 96 loop : -0.72 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 248 TYR 0.019 0.002 TYR A 62 PHE 0.011 0.002 PHE C 157 TRP 0.016 0.001 TRP a 386 HIS 0.006 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 ( 9996) covalent geometry : angle 0.79660 / 0.39 (13536) SS BOND : bond 0.00437 / 0.26 ( 21) SS BOND : angle 2.67425 / 1.59 ( 42) hydrogen bonds : bond 0.04493 / 2.98 ( 402) hydrogen bonds : angle 4.31919 / 3.06 ( 1044) link_ALPHA1-3 : bond 0.00485 / 0.22 ( 3) link_ALPHA1-3 : angle 1.35293 / 0.69 ( 9) link_ALPHA1-6 : bond 0.00405 / 0.26 ( 9) link_ALPHA1-6 : angle 1.61424 / 1.03 ( 27) link_BETA1-4 : bond 0.00776 / 0.44 ( 39) link_BETA1-4 : angle 2.93891 / 1.89 ( 117) link_BETA1-6 : bond 0.00093 / 0.04 ( 3) link_BETA1-6 : angle 1.83534 / 1.04 ( 9) link_NAG-ASN : bond 0.00302 / 0.20 ( 33) link_NAG-ASN : angle 2.72461 / 1.82 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 TYR cc_start: 0.6280 (m-10) cc_final: 0.5678 (m-10) REVERT: C 116 LYS cc_start: 0.8467 (mmtt) cc_final: 0.8095 (mmmt) REVERT: C 130 ASP cc_start: 0.8349 (t0) cc_final: 0.7787 (t0) REVERT: C 153 MET cc_start: 0.8480 (tmm) cc_final: 0.8151 (tmm) REVERT: c 303 GLU cc_start: 0.7720 (tp30) cc_final: 0.7471 (tp30) REVERT: c 410 MET cc_start: 0.7795 (ttm) cc_final: 0.6607 (ttt) REVERT: c 413 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8350 (tm-30) REVERT: c 418 GLU cc_start: 0.9182 (tm-30) cc_final: 0.8959 (mt-10) REVERT: A 66 TYR cc_start: 0.6712 (m-80) cc_final: 0.5827 (m-10) REVERT: A 130 ASP cc_start: 0.8016 (t0) cc_final: 0.7660 (t70) REVERT: A 153 MET cc_start: 0.8487 (tmm) cc_final: 0.8066 (tmm) REVERT: A 189 GLN cc_start: 0.8713 (mt0) cc_final: 0.8263 (mt0) REVERT: A 235 ARG cc_start: 0.8491 (ttm-80) cc_final: 0.7984 (ttm-80) REVERT: a 374 HIS cc_start: 0.8480 (t-90) cc_final: 0.8050 (t-90) REVERT: a 405 GLN cc_start: 0.9582 (tp40) cc_final: 0.9359 (tp-100) REVERT: a 410 MET cc_start: 0.8059 (ttm) cc_final: 0.7145 (ttt) REVERT: a 413 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8281 (tm-30) REVERT: B 62 TYR cc_start: 0.6856 (m-80) cc_final: 0.6547 (m-80) REVERT: B 66 TYR cc_start: 0.6711 (m-80) cc_final: 0.5975 (m-10) REVERT: B 75 MET cc_start: 0.8064 (mtm) cc_final: 0.7859 (mtm) REVERT: B 116 LYS cc_start: 0.8296 (mmtt) cc_final: 0.7425 (mmmt) REVERT: B 125 LYS cc_start: 0.9122 (mmtm) cc_final: 0.8877 (mmtm) REVERT: B 130 ASP cc_start: 0.8441 (t0) cc_final: 0.8028 (t0) REVERT: B 134 MET cc_start: 0.8583 (mmm) cc_final: 0.8319 (tmm) REVERT: B 189 GLN cc_start: 0.8782 (mt0) cc_final: 0.7659 (mt0) REVERT: B 210 TRP cc_start: 0.7564 (t-100) cc_final: 0.6491 (t-100) REVERT: b 303 GLU cc_start: 0.7992 (tp30) cc_final: 0.7471 (tp30) REVERT: b 374 HIS cc_start: 0.8466 (t-90) cc_final: 0.8155 (t-90) REVERT: b 405 GLN cc_start: 0.9527 (tp40) cc_final: 0.9294 (tp-100) REVERT: b 410 MET cc_start: 0.8115 (ttm) cc_final: 0.6977 (ttt) REVERT: b 413 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8230 (tm-30) REVERT: b 418 GLU cc_start: 0.9208 (tt0) cc_final: 0.8976 (tm-30) outliers start: 35 outliers final: 17 residues processed: 207 average time/residue: 0.1050 time to fit residues: 30.4236 Evaluate side-chains 192 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain b residue 270 GLU Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 402 ASP Chi-restraints excluded: chain b residue 419 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 90 ASN ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN A 247 GLN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.093804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.073038 restraints weight = 27197.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.075882 restraints weight = 15366.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.077931 restraints weight = 10889.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.079349 restraints weight = 8711.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.080238 restraints weight = 7483.994| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10104 Z= 0.157 Angle : 0.835 9.379 13839 Z= 0.391 Chirality : 0.046 0.273 1743 Planarity : 0.003 0.045 1593 Dihedral : 5.304 23.842 1167 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.28 % Allowed : 17.18 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.26), residues: 1074 helix: 0.94 (0.27), residues: 387 sheet: 0.53 (0.53), residues: 96 loop : -0.73 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 248 TYR 0.017 0.001 TYR b 371 PHE 0.011 0.001 PHE B 233 TRP 0.011 0.001 TRP a 386 HIS 0.005 0.001 HIS a 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 ( 9996) covalent geometry : angle 0.75964 / 0.37 (13536) SS BOND : bond 0.00325 / 0.20 ( 21) SS BOND : angle 2.17032 / 1.15 ( 42) hydrogen bonds : bond 0.04227 / 2.78 ( 402) hydrogen bonds : angle 4.21703 / 2.98 ( 1044) link_ALPHA1-3 : bond 0.00555 / 0.26 ( 3) link_ALPHA1-3 : angle 1.28446 / 0.67 ( 9) link_ALPHA1-6 : bond 0.00463 / 0.29 ( 9) link_ALPHA1-6 : angle 1.48120 / 0.94 ( 27) link_BETA1-4 : bond 0.00739 / 0.42 ( 39) link_BETA1-4 : angle 2.76743 / 1.77 ( 117) link_BETA1-6 : bond 0.00200 / 0.09 ( 3) link_BETA1-6 : angle 1.66099 / 0.95 ( 9) link_NAG-ASN : bond 0.00323 / 0.22 ( 33) link_NAG-ASN : angle 2.53499 / 1.68 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 TYR cc_start: 0.6114 (m-10) cc_final: 0.5553 (m-10) REVERT: C 116 LYS cc_start: 0.8481 (mmtt) cc_final: 0.8121 (mmmt) REVERT: C 130 ASP cc_start: 0.8311 (t0) cc_final: 0.7740 (t0) REVERT: C 153 MET cc_start: 0.8488 (tmm) cc_final: 0.7857 (tmm) REVERT: c 347 ASP cc_start: 0.8495 (p0) cc_final: 0.8161 (t0) REVERT: c 351 MET cc_start: 0.9155 (mmm) cc_final: 0.8830 (mmm) REVERT: c 410 MET cc_start: 0.7827 (ttm) cc_final: 0.6628 (ttt) REVERT: c 413 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8388 (tm-30) REVERT: c 418 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8960 (mt-10) REVERT: A 66 TYR cc_start: 0.6783 (m-80) cc_final: 0.5941 (m-10) REVERT: A 116 LYS cc_start: 0.8603 (mmtm) cc_final: 0.8091 (mmtt) REVERT: A 130 ASP cc_start: 0.8010 (t0) cc_final: 0.7657 (t70) REVERT: A 153 MET cc_start: 0.8496 (tmm) cc_final: 0.8089 (tmm) REVERT: A 189 GLN cc_start: 0.8739 (mt0) cc_final: 0.8273 (mt0) REVERT: A 194 MET cc_start: 0.9192 (tpp) cc_final: 0.8893 (tpt) REVERT: A 235 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.8027 (ttm-80) REVERT: A 244 LEU cc_start: 0.8956 (mt) cc_final: 0.8673 (mt) REVERT: a 347 ASP cc_start: 0.8356 (t70) cc_final: 0.8047 (t70) REVERT: a 348 GLN cc_start: 0.8715 (mp10) cc_final: 0.8308 (mt0) REVERT: a 351 MET cc_start: 0.9237 (tpp) cc_final: 0.8918 (mmm) REVERT: a 374 HIS cc_start: 0.8417 (t-90) cc_final: 0.8006 (t-90) REVERT: a 403 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8050 (tp) REVERT: a 405 GLN cc_start: 0.9555 (tp40) cc_final: 0.9355 (tp-100) REVERT: a 410 MET cc_start: 0.8053 (ttm) cc_final: 0.7046 (ttt) REVERT: a 413 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8269 (tm-30) REVERT: B 66 TYR cc_start: 0.6650 (m-80) cc_final: 0.5947 (m-10) REVERT: B 116 LYS cc_start: 0.8275 (mmtt) cc_final: 0.7440 (mmmt) REVERT: B 125 LYS cc_start: 0.9126 (mmtm) cc_final: 0.8886 (mmtm) REVERT: B 130 ASP cc_start: 0.8441 (t0) cc_final: 0.8032 (t0) REVERT: B 134 MET cc_start: 0.8607 (mmm) cc_final: 0.8248 (tmm) REVERT: B 189 GLN cc_start: 0.8793 (mt0) cc_final: 0.8357 (mm-40) REVERT: b 303 GLU cc_start: 0.8033 (tp30) cc_final: 0.7619 (tp30) REVERT: b 374 HIS cc_start: 0.8322 (t-90) cc_final: 0.8089 (t70) REVERT: b 405 GLN cc_start: 0.9527 (tp40) cc_final: 0.9283 (tp-100) REVERT: b 410 MET cc_start: 0.8094 (ttm) cc_final: 0.6974 (ttt) REVERT: b 413 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8272 (tm-30) REVERT: b 418 GLU cc_start: 0.9168 (tt0) cc_final: 0.8937 (tm-30) outliers start: 22 outliers final: 10 residues processed: 198 average time/residue: 0.1046 time to fit residues: 28.8499 Evaluate side-chains 190 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 179 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 63 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 3 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN B 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.091614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.071108 restraints weight = 26882.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.073865 restraints weight = 14950.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.075815 restraints weight = 10509.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.077140 restraints weight = 8399.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.077936 restraints weight = 7218.667| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10104 Z= 0.217 Angle : 0.875 8.824 13839 Z= 0.407 Chirality : 0.047 0.276 1743 Planarity : 0.004 0.044 1593 Dihedral : 5.317 24.182 1167 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 2.69 % Allowed : 16.87 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.26), residues: 1074 helix: 0.91 (0.28), residues: 387 sheet: 0.44 (0.54), residues: 96 loop : -0.88 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 248 TYR 0.017 0.002 TYR B 62 PHE 0.012 0.002 PHE B 157 TRP 0.017 0.001 TRP a 386 HIS 0.006 0.001 HIS C 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.22 ( 9996) covalent geometry : angle 0.80652 / 0.39 (13536) SS BOND : bond 0.00461 / 0.24 ( 21) SS BOND : angle 1.57581 / 0.96 ( 42) hydrogen bonds : bond 0.04453 / 2.93 ( 402) hydrogen bonds : angle 4.28482 / 3.03 ( 1044) link_ALPHA1-3 : bond 0.00481 / 0.22 ( 3) link_ALPHA1-3 : angle 1.38424 / 0.71 ( 9) link_ALPHA1-6 : bond 0.00375 / 0.23 ( 9) link_ALPHA1-6 : angle 1.65199 / 1.05 ( 27) link_BETA1-4 : bond 0.00697 / 0.40 ( 39) link_BETA1-4 : angle 2.75770 / 1.77 ( 117) link_BETA1-6 : bond 0.00035 / 0.02 ( 3) link_BETA1-6 : angle 1.86724 / 1.05 ( 9) link_NAG-ASN : bond 0.00279 / 0.19 ( 33) link_NAG-ASN : angle 2.62538 / 1.75 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 TYR cc_start: 0.6170 (m-10) cc_final: 0.5817 (m-10) REVERT: C 116 LYS cc_start: 0.8422 (mmtt) cc_final: 0.8220 (mmtt) REVERT: C 130 ASP cc_start: 0.8383 (t0) cc_final: 0.7856 (t0) REVERT: C 153 MET cc_start: 0.8424 (tmm) cc_final: 0.8075 (tmm) REVERT: c 303 GLU cc_start: 0.7777 (tp30) cc_final: 0.7346 (tp30) REVERT: c 347 ASP cc_start: 0.8493 (p0) cc_final: 0.8236 (t0) REVERT: c 351 MET cc_start: 0.9184 (mmm) cc_final: 0.8894 (mmm) REVERT: c 410 MET cc_start: 0.7968 (ttm) cc_final: 0.6823 (ttm) REVERT: c 413 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8416 (tm-30) REVERT: c 418 GLU cc_start: 0.9196 (tm-30) cc_final: 0.8964 (mt-10) REVERT: A 130 ASP cc_start: 0.8038 (t0) cc_final: 0.7632 (t70) REVERT: A 153 MET cc_start: 0.8477 (tmm) cc_final: 0.8007 (tmm) REVERT: A 189 GLN cc_start: 0.8728 (mt0) cc_final: 0.8259 (mt0) REVERT: A 235 ARG cc_start: 0.8360 (ttm-80) cc_final: 0.7869 (ttm-80) REVERT: a 278 TYR cc_start: 0.8808 (t80) cc_final: 0.8592 (t80) REVERT: a 287 GLU cc_start: 0.7693 (tp30) cc_final: 0.7473 (tp30) REVERT: a 351 MET cc_start: 0.9278 (tpp) cc_final: 0.8918 (mmm) REVERT: a 403 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8142 (tp) REVERT: a 405 GLN cc_start: 0.9531 (tp40) cc_final: 0.9269 (tp-100) REVERT: a 410 MET cc_start: 0.8147 (ttm) cc_final: 0.7869 (ttm) REVERT: a 413 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8365 (tm-30) REVERT: B 116 LYS cc_start: 0.8149 (mmtt) cc_final: 0.7323 (mmmt) REVERT: B 125 LYS cc_start: 0.9188 (mmtm) cc_final: 0.8980 (mmtm) REVERT: B 130 ASP cc_start: 0.8532 (t0) cc_final: 0.8153 (t0) REVERT: B 189 GLN cc_start: 0.8742 (mt0) cc_final: 0.8319 (mm-40) REVERT: b 303 GLU cc_start: 0.8064 (tp30) cc_final: 0.7518 (tp30) REVERT: b 374 HIS cc_start: 0.8405 (t-90) cc_final: 0.7937 (t-90) REVERT: b 405 GLN cc_start: 0.9490 (tp40) cc_final: 0.9280 (tp-100) REVERT: b 409 ASN cc_start: 0.9397 (m110) cc_final: 0.9131 (m-40) REVERT: b 413 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8267 (tm-30) REVERT: b 418 GLU cc_start: 0.9161 (tt0) cc_final: 0.8939 (tm-30) outliers start: 26 outliers final: 19 residues processed: 199 average time/residue: 0.1039 time to fit residues: 28.8082 Evaluate side-chains 189 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 90 ASN C 209 ASN ** c 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS B 209 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.094678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.074997 restraints weight = 27490.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.077585 restraints weight = 16878.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.079388 restraints weight = 12414.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.080616 restraints weight = 10197.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.081450 restraints weight = 8920.172| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.5838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10104 Z= 0.153 Angle : 0.821 8.296 13839 Z= 0.385 Chirality : 0.045 0.263 1743 Planarity : 0.003 0.045 1593 Dihedral : 5.212 27.654 1167 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.38 % Allowed : 17.29 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.26), residues: 1074 helix: 0.90 (0.28), residues: 387 sheet: 0.49 (0.54), residues: 96 loop : -0.84 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 248 TYR 0.017 0.001 TYR b 371 PHE 0.009 0.001 PHE B 233 TRP 0.025 0.001 TRP C 210 HIS 0.004 0.001 HIS c 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 9996) covalent geometry : angle 0.75829 / 0.37 (13536) SS BOND : bond 0.00327 / 0.20 ( 21) SS BOND : angle 1.36995 / 0.82 ( 42) hydrogen bonds : bond 0.04113 / 2.69 ( 402) hydrogen bonds : angle 4.19229 / 2.97 ( 1044) link_ALPHA1-3 : bond 0.00573 / 0.27 ( 3) link_ALPHA1-3 : angle 1.29537 / 0.67 ( 9) link_ALPHA1-6 : bond 0.00468 / 0.30 ( 9) link_ALPHA1-6 : angle 1.46622 / 0.93 ( 27) link_BETA1-4 : bond 0.00711 / 0.41 ( 39) link_BETA1-4 : angle 2.60428 / 1.67 ( 117) link_BETA1-6 : bond 0.00209 / 0.10 ( 3) link_BETA1-6 : angle 1.62763 / 0.93 ( 9) link_NAG-ASN : bond 0.00319 / 0.22 ( 33) link_NAG-ASN : angle 2.39121 / 1.59 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8079 (mmtt) cc_final: 0.7683 (mmmt) REVERT: C 130 ASP cc_start: 0.8601 (t0) cc_final: 0.8088 (t0) REVERT: C 153 MET cc_start: 0.8510 (tmm) cc_final: 0.7946 (tmm) REVERT: C 194 MET cc_start: 0.8999 (tpt) cc_final: 0.8771 (tpt) REVERT: C 246 SER cc_start: 0.8525 (p) cc_final: 0.7532 (p) REVERT: C 248 ARG cc_start: 0.7315 (tpt170) cc_final: 0.6696 (tpm170) REVERT: c 303 GLU cc_start: 0.7883 (tp30) cc_final: 0.7602 (tp30) REVERT: c 351 MET cc_start: 0.8991 (mmm) cc_final: 0.8703 (mmm) REVERT: c 413 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8240 (tm-30) REVERT: A 66 TYR cc_start: 0.6825 (m-80) cc_final: 0.6065 (m-10) REVERT: A 116 LYS cc_start: 0.8262 (mmtm) cc_final: 0.7600 (mmtt) REVERT: A 130 ASP cc_start: 0.8134 (t0) cc_final: 0.7795 (t70) REVERT: A 153 MET cc_start: 0.8539 (tmm) cc_final: 0.8145 (tmm) REVERT: A 235 ARG cc_start: 0.8330 (ttm-80) cc_final: 0.8001 (ttm-80) REVERT: a 351 MET cc_start: 0.9121 (tpp) cc_final: 0.8815 (mmm) REVERT: a 403 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8209 (tp) REVERT: a 410 MET cc_start: 0.8065 (ttm) cc_final: 0.6578 (ttt) REVERT: a 413 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8246 (tm-30) REVERT: B 66 TYR cc_start: 0.6677 (m-80) cc_final: 0.6141 (m-10) REVERT: B 116 LYS cc_start: 0.7874 (mmtt) cc_final: 0.7187 (mtpt) REVERT: B 130 ASP cc_start: 0.8693 (t0) cc_final: 0.8449 (t0) REVERT: B 189 GLN cc_start: 0.8674 (mt0) cc_final: 0.8370 (mm-40) REVERT: b 332 MET cc_start: 0.7349 (mmm) cc_final: 0.7148 (tpp) REVERT: b 409 ASN cc_start: 0.9327 (m110) cc_final: 0.9079 (m-40) REVERT: b 410 MET cc_start: 0.8137 (ttm) cc_final: 0.7086 (ttt) REVERT: b 413 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8186 (tm-30) REVERT: b 414 MET cc_start: 0.8149 (tmm) cc_final: 0.7849 (ttm) REVERT: b 418 GLU cc_start: 0.9122 (tt0) cc_final: 0.8667 (mt-10) outliers start: 23 outliers final: 17 residues processed: 195 average time/residue: 0.1093 time to fit residues: 29.4848 Evaluate side-chains 194 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain c residue 349 LEU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain a residue 417 LYS Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 47 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 81 optimal weight: 0.3980 chunk 85 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 84 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 324 GLN A 90 ASN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 354 HIS b 405 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.095315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.076041 restraints weight = 27174.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.078667 restraints weight = 16180.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.080488 restraints weight = 11744.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.081718 restraints weight = 9563.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.082566 restraints weight = 8294.199| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10104 Z= 0.147 Angle : 0.814 7.929 13839 Z= 0.383 Chirality : 0.044 0.253 1743 Planarity : 0.003 0.046 1593 Dihedral : 5.155 25.482 1167 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.17 % Allowed : 18.63 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.26), residues: 1074 helix: 0.95 (0.27), residues: 384 sheet: 0.55 (0.55), residues: 96 loop : -0.81 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 248 TYR 0.030 0.001 TYR a 371 PHE 0.010 0.001 PHE B 233 TRP 0.023 0.001 TRP C 210 HIS 0.007 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 9996) covalent geometry : angle 0.75469 / 0.37 (13536) SS BOND : bond 0.00260 / 0.16 ( 21) SS BOND : angle 1.43297 / 0.87 ( 42) hydrogen bonds : bond 0.04044 / 2.65 ( 402) hydrogen bonds : angle 4.21824 / 2.96 ( 1044) link_ALPHA1-3 : bond 0.00593 / 0.28 ( 3) link_ALPHA1-3 : angle 1.31388 / 0.68 ( 9) link_ALPHA1-6 : bond 0.00471 / 0.30 ( 9) link_ALPHA1-6 : angle 1.44955 / 0.92 ( 27) link_BETA1-4 : bond 0.00690 / 0.40 ( 39) link_BETA1-4 : angle 2.49805 / 1.60 ( 117) link_BETA1-6 : bond 0.00232 / 0.11 ( 3) link_BETA1-6 : angle 1.50558 / 0.86 ( 9) link_NAG-ASN : bond 0.00434 / 0.26 ( 33) link_NAG-ASN : angle 2.36907 / 1.57 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8116 (mmtt) cc_final: 0.7695 (mmmt) REVERT: C 130 ASP cc_start: 0.8525 (t0) cc_final: 0.7999 (t0) REVERT: C 134 MET cc_start: 0.8400 (mmm) cc_final: 0.7807 (tmm) REVERT: C 153 MET cc_start: 0.8507 (tmm) cc_final: 0.7946 (tmm) REVERT: C 194 MET cc_start: 0.9038 (tpt) cc_final: 0.8817 (tpt) REVERT: c 287 GLU cc_start: 0.7828 (tp30) cc_final: 0.7599 (tp30) REVERT: c 303 GLU cc_start: 0.7864 (tp30) cc_final: 0.7557 (tp30) REVERT: c 413 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8316 (tm-30) REVERT: A 66 TYR cc_start: 0.6699 (m-80) cc_final: 0.6056 (m-10) REVERT: A 130 ASP cc_start: 0.8140 (t0) cc_final: 0.7799 (t70) REVERT: A 153 MET cc_start: 0.8415 (tmm) cc_final: 0.7650 (tmm) REVERT: A 235 ARG cc_start: 0.8380 (ttm-80) cc_final: 0.8041 (ttm-80) REVERT: a 303 GLU cc_start: 0.7802 (tp30) cc_final: 0.7574 (tp30) REVERT: a 351 MET cc_start: 0.9142 (tpp) cc_final: 0.8813 (mmm) REVERT: a 403 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8212 (tp) REVERT: a 410 MET cc_start: 0.8101 (ttm) cc_final: 0.6636 (ttt) REVERT: a 413 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8257 (tm-30) REVERT: B 66 TYR cc_start: 0.6582 (m-80) cc_final: 0.6161 (m-10) REVERT: B 116 LYS cc_start: 0.7891 (mmtt) cc_final: 0.7175 (mtpt) REVERT: B 130 ASP cc_start: 0.8558 (t0) cc_final: 0.8261 (t0) REVERT: B 189 GLN cc_start: 0.8722 (mt0) cc_final: 0.8294 (mt0) REVERT: b 311 ASP cc_start: 0.8941 (m-30) cc_final: 0.8460 (t0) REVERT: b 410 MET cc_start: 0.8128 (ttm) cc_final: 0.7102 (ttt) REVERT: b 413 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8201 (tm-30) REVERT: b 418 GLU cc_start: 0.9091 (tt0) cc_final: 0.8869 (tm-30) outliers start: 21 outliers final: 16 residues processed: 193 average time/residue: 0.1012 time to fit residues: 27.1244 Evaluate side-chains 187 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain c residue 349 LEU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 81 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 90 ASN A 90 ASN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 342 ASN b 405 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.095495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.076211 restraints weight = 27134.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.078819 restraints weight = 16283.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.080659 restraints weight = 11851.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.081896 restraints weight = 9634.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.082742 restraints weight = 8367.048| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.6106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10104 Z= 0.153 Angle : 0.836 8.662 13839 Z= 0.396 Chirality : 0.045 0.242 1743 Planarity : 0.004 0.046 1593 Dihedral : 5.149 25.174 1167 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 2.28 % Allowed : 18.94 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.26), residues: 1074 helix: 0.86 (0.27), residues: 384 sheet: 0.62 (0.56), residues: 96 loop : -0.80 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 248 TYR 0.026 0.001 TYR a 371 PHE 0.010 0.001 PHE B 233 TRP 0.027 0.001 TRP C 210 HIS 0.006 0.001 HIS a 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 9996) covalent geometry : angle 0.78157 / 0.39 (13536) SS BOND : bond 0.00305 / 0.18 ( 21) SS BOND : angle 1.49439 / 0.86 ( 42) hydrogen bonds : bond 0.04122 / 2.72 ( 402) hydrogen bonds : angle 4.30627 / 3.04 ( 1044) link_ALPHA1-3 : bond 0.00571 / 0.27 ( 3) link_ALPHA1-3 : angle 1.30900 / 0.68 ( 9) link_ALPHA1-6 : bond 0.00465 / 0.30 ( 9) link_ALPHA1-6 : angle 1.46262 / 0.93 ( 27) link_BETA1-4 : bond 0.00711 / 0.41 ( 39) link_BETA1-4 : angle 2.42646 / 1.56 ( 117) link_BETA1-6 : bond 0.00208 / 0.10 ( 3) link_BETA1-6 : angle 1.50146 / 0.85 ( 9) link_NAG-ASN : bond 0.00294 / 0.19 ( 33) link_NAG-ASN : angle 2.30498 / 1.53 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7644 (mmmt) REVERT: C 130 ASP cc_start: 0.8503 (t0) cc_final: 0.7948 (t0) REVERT: C 153 MET cc_start: 0.8506 (tmm) cc_final: 0.7952 (tmm) REVERT: c 413 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8390 (tm-30) REVERT: A 66 TYR cc_start: 0.6744 (m-80) cc_final: 0.6094 (m-10) REVERT: A 75 MET cc_start: 0.9057 (mmm) cc_final: 0.8850 (tpp) REVERT: A 116 LYS cc_start: 0.8411 (mmtm) cc_final: 0.7719 (mmtt) REVERT: A 130 ASP cc_start: 0.8150 (t0) cc_final: 0.7786 (t70) REVERT: A 134 MET cc_start: 0.8335 (mmm) cc_final: 0.8128 (tpt) REVERT: A 153 MET cc_start: 0.8389 (tmm) cc_final: 0.7650 (tmm) REVERT: A 235 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.8005 (ttm-80) REVERT: a 351 MET cc_start: 0.9167 (tpp) cc_final: 0.8851 (mmm) REVERT: a 403 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8230 (tp) REVERT: a 410 MET cc_start: 0.8121 (ttm) cc_final: 0.6639 (ttt) REVERT: a 413 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8266 (tm-30) REVERT: B 66 TYR cc_start: 0.6635 (m-80) cc_final: 0.6325 (m-10) REVERT: B 116 LYS cc_start: 0.7873 (mmtt) cc_final: 0.7189 (mtpt) REVERT: B 130 ASP cc_start: 0.8584 (t0) cc_final: 0.8284 (t0) REVERT: b 347 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7591 (t70) REVERT: b 359 MET cc_start: 0.9073 (tpp) cc_final: 0.8802 (ttp) REVERT: b 410 MET cc_start: 0.8122 (ttm) cc_final: 0.7076 (ttt) REVERT: b 413 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8222 (tm-30) REVERT: b 414 MET cc_start: 0.8114 (tmm) cc_final: 0.7816 (ttm) REVERT: b 418 GLU cc_start: 0.9103 (tt0) cc_final: 0.8644 (mt-10) outliers start: 22 outliers final: 14 residues processed: 195 average time/residue: 0.1078 time to fit residues: 28.8698 Evaluate side-chains 189 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain c residue 349 LEU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 402 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 402 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 77 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 55 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 90 ASN A 90 ASN a 331 GLN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.095827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.076423 restraints weight = 27304.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.079031 restraints weight = 16388.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.080825 restraints weight = 11950.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.082039 restraints weight = 9745.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.082876 restraints weight = 8485.821| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10104 Z= 0.159 Angle : 0.852 12.966 13839 Z= 0.402 Chirality : 0.045 0.241 1743 Planarity : 0.004 0.094 1593 Dihedral : 5.167 24.890 1167 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 2.07 % Allowed : 19.88 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.26), residues: 1074 helix: 0.86 (0.27), residues: 384 sheet: 0.75 (0.57), residues: 96 loop : -0.79 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 248 TYR 0.028 0.001 TYR B 62 PHE 0.009 0.001 PHE B 233 TRP 0.026 0.001 TRP C 210 HIS 0.006 0.001 HIS a 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 9996) covalent geometry : angle 0.79958 / 0.39 (13536) SS BOND : bond 0.00289 / 0.17 ( 21) SS BOND : angle 1.55524 / 0.91 ( 42) hydrogen bonds : bond 0.04159 / 2.74 ( 402) hydrogen bonds : angle 4.34964 / 3.07 ( 1044) link_ALPHA1-3 : bond 0.00582 / 0.27 ( 3) link_ALPHA1-3 : angle 1.31651 / 0.68 ( 9) link_ALPHA1-6 : bond 0.00452 / 0.29 ( 9) link_ALPHA1-6 : angle 1.46626 / 0.93 ( 27) link_BETA1-4 : bond 0.00687 / 0.39 ( 39) link_BETA1-4 : angle 2.40812 / 1.55 ( 117) link_BETA1-6 : bond 0.00192 / 0.09 ( 3) link_BETA1-6 : angle 1.49808 / 0.85 ( 9) link_NAG-ASN : bond 0.00297 / 0.19 ( 33) link_NAG-ASN : angle 2.29926 / 1.54 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1681.22 seconds wall clock time: 30 minutes 13.05 seconds (1813.05 seconds total)