Starting phenix.real_space_refine on Wed Sep 17 17:18:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ck7_45643/09_2025/9ck7_45643.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ck7_45643/09_2025/9ck7_45643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ck7_45643/09_2025/9ck7_45643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ck7_45643/09_2025/9ck7_45643.map" model { file = "/net/cci-nas-00/data/ceres_data/9ck7_45643/09_2025/9ck7_45643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ck7_45643/09_2025/9ck7_45643.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 6246 2.51 5 N 1649 2.21 5 O 2041 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10026 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1520 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "B" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1520 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "C" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1520 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "H" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 595 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'TRANS': 118} Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 119 Planarities with less than four sites: {'UNK:plan-1': 119} Unresolved non-hydrogen planarities: 119 Chain: "L" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 575 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'TRANS': 114} Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 115 Planarities with less than four sites: {'UNK:plan-1': 115} Unresolved non-hydrogen planarities: 115 Chain: "a" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1171 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain breaks: 2 Chain: "b" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1173 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain breaks: 2 Chain: "c" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1163 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.42, per 1000 atoms: 0.24 Number of scatterers: 10026 At special positions: 0 Unit cell: (123.25, 88.45, 95.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2041 8.00 N 1649 7.00 C 6246 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.04 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.04 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.03 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.03 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.02 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.03 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN U 4 " - " MAN U 5 " ALPHA1-3 " BMA U 3 " - " MAN U 4 " ALPHA1-6 " BMA J 3 " - " MAN J 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG N 1 " - " FUC N 3 " NAG-ASN " NAG A 301 " - " ASN A 89 " " NAG A 302 " - " ASN A 99 " " NAG B 301 " - " ASN B 89 " " NAG B 302 " - " ASN B 224 " " NAG C 301 " - " ASN C 99 " " NAG C 302 " - " ASN C 119 " " NAG C 303 " - " ASN C 89 " " NAG D 1 " - " ASN A 109 " " NAG E 1 " - " ASN A 119 " " NAG F 1 " - " ASN A 79 " " NAG G 1 " - " ASN A 167 " " NAG I 1 " - " ASN A 224 " " NAG J 1 " - " ASN B 79 " " NAG K 1 " - " ASN B 99 " " NAG M 1 " - " ASN B 109 " " NAG N 1 " - " ASN B 119 " " NAG O 1 " - " ASN B 167 " " NAG P 1 " - " ASN C 79 " " NAG Q 1 " - " ASN C 109 " " NAG R 1 " - " ASN C 167 " " NAG S 1 " - " ASN C 224 " " NAG T 1 " - " ASN a 365 " " NAG U 1 " - " ASN b 365 " " NAG V 1 " - " ASN b 373 " " NAG W 1 " - " ASN c 365 " " NAG a 701 " - " ASN a 373 " " NAG a 702 " - " ASN a 390 " " NAG a 703 " - " ASN a 395 " " NAG b 701 " - " ASN b 395 " " NAG b 702 " - " ASN b 390 " " NAG c 701 " - " ASN c 373 " " NAG c 702 " - " ASN c 390 " " NAG c 703 " - " ASN c 395 " Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 313.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 15 sheets defined 38.9% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.812A pdb=" N THR A 77 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.985A pdb=" N GLY A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 4.503A pdb=" N ILE A 201 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 203 " --> pdb=" O TYR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.712A pdb=" N SER A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.949A pdb=" N THR B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N MET B 80 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.631A pdb=" N GLY B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 248 removed outlier: 3.973A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.527A pdb=" N LEU C 78 " --> pdb=" O MET C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 130 through 144 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 182 through 195 removed outlier: 3.966A pdb=" N GLY C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 238 through 246 removed outlier: 4.306A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'a' and resid 281 through 285 removed outlier: 3.658A pdb=" N LEU a 285 " --> pdb=" O ARG a 282 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 304 removed outlier: 3.797A pdb=" N VAL a 298 " --> pdb=" O GLY a 294 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU a 303 " --> pdb=" O ALA a 299 " (cutoff:3.500A) Processing helix chain 'a' and resid 307 through 326 removed outlier: 3.874A pdb=" N ASP a 311 " --> pdb=" O GLU a 307 " (cutoff:3.500A) Processing helix chain 'a' and resid 334 through 345 removed outlier: 6.097A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ALA a 343 " --> pdb=" O LYS a 339 " (cutoff:3.500A) Processing helix chain 'a' and resid 348 through 359 Processing helix chain 'a' and resid 399 through 412 removed outlier: 3.507A pdb=" N ILE a 403 " --> pdb=" O PHE a 399 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR a 412 " --> pdb=" O ASP a 408 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 304 Processing helix chain 'b' and resid 307 through 325 removed outlier: 4.144A pdb=" N ASP b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) Processing helix chain 'b' and resid 334 through 345 removed outlier: 5.490A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.622A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 399 through 412 removed outlier: 3.776A pdb=" N ILE b 403 " --> pdb=" O PHE b 399 " (cutoff:3.500A) Processing helix chain 'c' and resid 281 through 285 removed outlier: 3.605A pdb=" N LEU c 285 " --> pdb=" O ARG c 282 " (cutoff:3.500A) Processing helix chain 'c' and resid 294 through 304 removed outlier: 3.669A pdb=" N VAL c 298 " --> pdb=" O GLY c 294 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS c 301 " --> pdb=" O ALA c 297 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN c 302 " --> pdb=" O VAL c 298 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU c 303 " --> pdb=" O ALA c 299 " (cutoff:3.500A) Processing helix chain 'c' and resid 311 through 325 Processing helix chain 'c' and resid 334 through 345 removed outlier: 5.464A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.696A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 399 through 412 removed outlier: 3.586A pdb=" N THR c 412 " --> pdb=" O ASP c 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 3.764A pdb=" N GLU A 67 " --> pdb=" O ASN a 373 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN a 373 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 69 " --> pdb=" O TYR a 371 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR a 371 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 87 Processing sheet with id=AA3, first strand: chain 'B' and resid 66 through 72 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 87 removed outlier: 7.432A pdb=" N THR B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AA6, first strand: chain 'C' and resid 84 through 87 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 4 removed outlier: 3.857A pdb=" N UNK H 3 " --> pdb=" O UNK H 25 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N UNK H 76 " --> pdb=" O UNK H 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 45 through 51 removed outlier: 4.805A pdb=" N UNK H 47 " --> pdb=" O UNK H 38 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N UNK H 38 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N UNK H 49 " --> pdb=" O UNK H 36 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N UNK H 90 " --> pdb=" O UNK H 105 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N UNK H 105 " --> pdb=" O UNK H 90 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N UNK H 92 " --> pdb=" O UNK H 103 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N UNK H 103 " --> pdb=" O UNK H 92 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N UNK H 94 " --> pdb=" O UNK H 101 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N UNK H 100F" --> pdb=" O UNK H 96 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.858A pdb=" N UNK L 11 " --> pdb=" O UNK L 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB2, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.569A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 279 through 280 Processing sheet with id=AB4, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AB5, first strand: chain 'b' and resid 388 through 389 Processing sheet with id=AB6, first strand: chain 'c' and resid 388 through 389 356 hydrogen bonds defined for protein. 945 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: 1.29 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2571 1.33 - 1.46: 3159 1.46 - 1.59: 4324 1.59 - 1.72: 0 1.72 - 1.85: 138 Bond restraints: 10192 Sorted by residual: bond pdb=" N HIS B 230 " pdb=" CA HIS B 230 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.17e-02 7.31e+03 9.49e+00 bond pdb=" N GLU B 228 " pdb=" CA GLU B 228 " ideal model delta sigma weight residual 1.455 1.486 -0.030 1.09e-02 8.42e+03 7.81e+00 bond pdb=" N PHE B 233 " pdb=" CA PHE B 233 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.28e-02 6.10e+03 6.99e+00 bond pdb=" N ASN B 146 " pdb=" CA ASN B 146 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.29e-02 6.01e+03 5.17e+00 bond pdb=" N GLN B 232 " pdb=" CA GLN B 232 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 5.04e+00 ... (remaining 10187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 12938 1.79 - 3.58: 714 3.58 - 5.36: 143 5.36 - 7.15: 35 7.15 - 8.94: 5 Bond angle restraints: 13835 Sorted by residual: angle pdb=" CA ASP B 229 " pdb=" C ASP B 229 " pdb=" O ASP B 229 " ideal model delta sigma weight residual 122.64 117.77 4.87 1.25e+00 6.40e-01 1.52e+01 angle pdb=" CB GLN b 405 " pdb=" CG GLN b 405 " pdb=" CD GLN b 405 " ideal model delta sigma weight residual 112.60 118.92 -6.32 1.70e+00 3.46e-01 1.38e+01 angle pdb=" CA GLU B 100 " pdb=" CB GLU B 100 " pdb=" CG GLU B 100 " ideal model delta sigma weight residual 114.10 120.98 -6.88 2.00e+00 2.50e-01 1.18e+01 angle pdb=" C PRO B 145 " pdb=" N ASN B 146 " pdb=" CA ASN B 146 " ideal model delta sigma weight residual 121.54 127.92 -6.38 1.91e+00 2.74e-01 1.12e+01 angle pdb=" CA GLN B 232 " pdb=" C GLN B 232 " pdb=" O GLN B 232 " ideal model delta sigma weight residual 120.55 117.02 3.53 1.06e+00 8.90e-01 1.11e+01 ... (remaining 13830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.80: 6454 21.80 - 43.61: 296 43.61 - 65.41: 56 65.41 - 87.21: 24 87.21 - 109.02: 9 Dihedral angle restraints: 6839 sinusoidal: 3206 harmonic: 3633 Sorted by residual: 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 -162.05 76.05 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" CB CYS A 180 " pdb=" SG CYS A 180 " pdb=" SG CYS A 212 " pdb=" CB CYS A 212 " ideal model delta sinusoidal sigma weight residual 93.00 155.37 -62.37 1 1.00e+01 1.00e-02 5.15e+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 -134.05 48.05 1 1.00e+01 1.00e-02 3.18e+01 ... (remaining 6836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1716 0.134 - 0.267: 31 0.267 - 0.400: 4 0.400 - 0.534: 4 0.534 - 0.667: 2 Chirality restraints: 1757 Sorted by residual: chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-02 2.50e+03 6.32e+02 chirality pdb=" C1 MAN J 4 " pdb=" O6 BMA J 3 " pdb=" C2 MAN J 4 " pdb=" O5 MAN J 4 " both_signs ideal model delta sigma weight residual False 2.40 1.95 0.45 2.00e-02 2.50e+03 5.01e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.41e+02 ... (remaining 1754 not shown) Planarity restraints: 1718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 701 " 0.359 2.00e-02 2.50e+03 3.09e-01 1.19e+03 pdb=" C7 NAG b 701 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG b 701 " 0.086 2.00e-02 2.50e+03 pdb=" N2 NAG b 701 " -0.546 2.00e-02 2.50e+03 pdb=" O7 NAG b 701 " 0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.351 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG F 1 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.147 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.533 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " 0.340 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG J 2 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " 0.069 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " -0.519 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " 0.187 2.00e-02 2.50e+03 ... (remaining 1715 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 200 2.66 - 3.22: 9560 3.22 - 3.78: 14699 3.78 - 4.34: 19838 4.34 - 4.90: 33289 Nonbonded interactions: 77586 Sorted by model distance: nonbonded pdb=" OG1 THR A 81 " pdb=" OD1 ASN a 319 " model vdw 2.103 3.040 nonbonded pdb=" O ASN a 409 " pdb=" OG1 THR a 412 " model vdw 2.119 3.040 nonbonded pdb=" OG SER b 367 " pdb=" OH TYR b 393 " model vdw 2.120 3.040 nonbonded pdb=" OG SER B 169 " pdb=" OE1 GLN B 218 " model vdw 2.153 3.040 nonbonded pdb=" OG1 THR C 226 " pdb=" OE2 GLU C 228 " model vdw 2.227 3.040 ... (remaining 77581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 60 through 302) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'E' selection = chain 'N' } ncs_group { reference = (chain 'H' and resid 6 through 109) selection = chain 'L' } ncs_group { reference = (chain 'a' and (resid 260 through 267 or resid 278 through 702)) selection = (chain 'b' and (resid 260 through 267 or resid 278 through 702)) selection = (chain 'c' and (resid 260 through 267 or resid 278 through 702)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.960 Find NCS groups from input model: 0.250 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 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 : 0.005 0.054 10271 Z= 0.255 Angle : 1.035 13.836 14051 Z= 0.482 Chirality : 0.056 0.667 1757 Planarity : 0.020 0.309 1685 Dihedral : 13.788 109.016 4412 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.11 % Allowed : 1.21 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.26), residues: 971 helix: 0.21 (0.27), residues: 321 sheet: -2.19 (0.37), residues: 151 loop : -1.24 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG a 282 TYR 0.024 0.002 TYR C 253 PHE 0.015 0.002 PHE b 262 TRP 0.034 0.001 TRP A 196 HIS 0.020 0.002 HIS b 354 Details of bonding type rmsd covalent geometry : bond 0.00534 (10192) covalent geometry : angle 0.96460 (13835) SS BOND : bond 0.00325 ( 21) SS BOND : angle 1.74485 ( 42) hydrogen bonds : bond 0.16994 ( 356) hydrogen bonds : angle 6.88027 ( 945) link_ALPHA1-2 : bond 0.00227 ( 1) link_ALPHA1-2 : angle 3.19311 ( 3) link_ALPHA1-3 : bond 0.00185 ( 1) link_ALPHA1-3 : angle 4.11204 ( 3) link_ALPHA1-6 : bond 0.00660 ( 1) link_ALPHA1-6 : angle 2.74621 ( 3) link_BETA1-4 : bond 0.01213 ( 20) link_BETA1-4 : angle 4.01372 ( 60) link_BETA1-6 : bond 0.00520 ( 2) link_BETA1-6 : angle 1.10723 ( 6) link_NAG-ASN : bond 0.00760 ( 33) link_NAG-ASN : angle 3.15547 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 242 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 THR cc_start: 0.8439 (p) cc_final: 0.7900 (p) REVERT: B 76 GLU cc_start: 0.8152 (tp30) cc_final: 0.7772 (tp30) REVERT: B 80 MET cc_start: 0.7550 (ttt) cc_final: 0.6996 (mtp) REVERT: C 76 GLU cc_start: 0.7680 (tt0) cc_final: 0.7192 (tm-30) REVERT: C 194 MET cc_start: 0.8460 (tpp) cc_final: 0.7945 (tpt) REVERT: b 283 TRP cc_start: 0.7533 (m-90) cc_final: 0.7186 (m-90) REVERT: b 371 TYR cc_start: 0.8689 (p90) cc_final: 0.8194 (p90) REVERT: c 286 ILE cc_start: 0.7288 (mm) cc_final: 0.7051 (mp) outliers start: 1 outliers final: 1 residues processed: 243 average time/residue: 0.0933 time to fit residues: 32.6007 Evaluate side-chains 215 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 395 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN C 223 GLN a 319 ASN a 335 GLN b 348 GLN ** b 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 305 HIS c 348 GLN c 354 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.205010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.176272 restraints weight = 13299.918| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.96 r_work: 0.3988 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10271 Z= 0.144 Angle : 0.828 18.857 14051 Z= 0.360 Chirality : 0.047 0.534 1757 Planarity : 0.004 0.042 1685 Dihedral : 9.658 81.922 2507 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.09 % Allowed : 8.80 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.27), residues: 971 helix: 0.42 (0.28), residues: 333 sheet: -1.95 (0.39), residues: 143 loop : -1.07 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 282 TYR 0.025 0.001 TYR c 363 PHE 0.017 0.001 PHE c 318 TRP 0.021 0.001 TRP A 196 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00297 (10192) covalent geometry : angle 0.73089 (13835) SS BOND : bond 0.00407 ( 21) SS BOND : angle 1.28808 ( 42) hydrogen bonds : bond 0.04005 ( 356) hydrogen bonds : angle 5.26697 ( 945) link_ALPHA1-2 : bond 0.00539 ( 1) link_ALPHA1-2 : angle 2.06069 ( 3) link_ALPHA1-3 : bond 0.00333 ( 1) link_ALPHA1-3 : angle 5.22342 ( 3) link_ALPHA1-6 : bond 0.01839 ( 1) link_ALPHA1-6 : angle 1.69446 ( 3) link_BETA1-4 : bond 0.01160 ( 20) link_BETA1-4 : angle 3.13067 ( 60) link_BETA1-6 : bond 0.00399 ( 2) link_BETA1-6 : angle 1.21274 ( 6) link_NAG-ASN : bond 0.01004 ( 33) link_NAG-ASN : angle 3.85463 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 THR cc_start: 0.8443 (p) cc_final: 0.8136 (p) REVERT: C 194 MET cc_start: 0.8248 (tpp) cc_final: 0.7858 (tpt) REVERT: b 357 ASP cc_start: 0.8310 (t0) cc_final: 0.8067 (t70) REVERT: b 371 TYR cc_start: 0.8623 (p90) cc_final: 0.8025 (p90) REVERT: c 286 ILE cc_start: 0.7313 (mm) cc_final: 0.7105 (mp) outliers start: 19 outliers final: 14 residues processed: 215 average time/residue: 0.1013 time to fit residues: 30.7387 Evaluate side-chains 210 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 196 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 397 THR Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 348 GLN Chi-restraints excluded: chain c residue 395 ASN Chi-restraints excluded: chain c residue 398 HIS Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 52 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 108 optimal weight: 0.5980 chunk 69 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 305 HIS b 348 GLN ** b 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.196509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.166156 restraints weight = 13353.719| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 3.08 r_work: 0.3867 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 10271 Z= 0.240 Angle : 0.864 13.351 14051 Z= 0.382 Chirality : 0.048 0.373 1757 Planarity : 0.004 0.044 1685 Dihedral : 8.858 60.516 2507 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.63 % Allowed : 10.89 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.27), residues: 971 helix: 0.60 (0.28), residues: 328 sheet: -2.04 (0.39), residues: 143 loop : -1.10 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG c 314 TYR 0.024 0.002 TYR c 363 PHE 0.015 0.002 PHE a 309 TRP 0.029 0.002 TRP A 196 HIS 0.006 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00550 (10192) covalent geometry : angle 0.77613 (13835) SS BOND : bond 0.00493 ( 21) SS BOND : angle 1.58246 ( 42) hydrogen bonds : bond 0.03802 ( 356) hydrogen bonds : angle 5.14345 ( 945) link_ALPHA1-2 : bond 0.00534 ( 1) link_ALPHA1-2 : angle 2.18231 ( 3) link_ALPHA1-3 : bond 0.00008 ( 1) link_ALPHA1-3 : angle 5.10601 ( 3) link_ALPHA1-6 : bond 0.01569 ( 1) link_ALPHA1-6 : angle 1.23334 ( 3) link_BETA1-4 : bond 0.01085 ( 20) link_BETA1-4 : angle 3.10515 ( 60) link_BETA1-6 : bond 0.00249 ( 2) link_BETA1-6 : angle 1.52114 ( 6) link_NAG-ASN : bond 0.00734 ( 33) link_NAG-ASN : angle 3.69828 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8474 (mttp) cc_final: 0.8241 (mtpt) REVERT: A 239 ILE cc_start: 0.9017 (mm) cc_final: 0.8786 (pt) REVERT: B 120 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8233 (tt) REVERT: C 194 MET cc_start: 0.8375 (tpp) cc_final: 0.7870 (tpt) REVERT: b 321 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.6639 (mp-120) REVERT: b 371 TYR cc_start: 0.8791 (p90) cc_final: 0.8284 (p90) REVERT: c 307 GLU cc_start: 0.6166 (tm-30) cc_final: 0.5835 (tm-30) outliers start: 33 outliers final: 23 residues processed: 228 average time/residue: 0.0918 time to fit residues: 30.5498 Evaluate side-chains 229 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 397 THR Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 336 LEU Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 395 ASN Chi-restraints excluded: chain c residue 398 HIS Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 93 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 39 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 348 GLN ** b 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 348 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.197185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.167752 restraints weight = 13390.550| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 3.03 r_work: 0.3896 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10271 Z= 0.150 Angle : 0.755 13.085 14051 Z= 0.334 Chirality : 0.044 0.357 1757 Planarity : 0.004 0.040 1685 Dihedral : 8.002 58.549 2507 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.30 % Allowed : 14.85 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.27), residues: 971 helix: 0.83 (0.29), residues: 328 sheet: -2.05 (0.39), residues: 143 loop : -0.98 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG c 325 TYR 0.027 0.001 TYR c 363 PHE 0.012 0.001 PHE c 318 TRP 0.028 0.001 TRP A 196 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00332 (10192) covalent geometry : angle 0.66908 (13835) SS BOND : bond 0.00766 ( 21) SS BOND : angle 1.21809 ( 42) hydrogen bonds : bond 0.03261 ( 356) hydrogen bonds : angle 4.82968 ( 945) link_ALPHA1-2 : bond 0.00900 ( 1) link_ALPHA1-2 : angle 2.05014 ( 3) link_ALPHA1-3 : bond 0.00097 ( 1) link_ALPHA1-3 : angle 5.44808 ( 3) link_ALPHA1-6 : bond 0.01515 ( 1) link_ALPHA1-6 : angle 1.22793 ( 3) link_BETA1-4 : bond 0.01076 ( 20) link_BETA1-4 : angle 2.98501 ( 60) link_BETA1-6 : bond 0.00306 ( 2) link_BETA1-6 : angle 1.37454 ( 6) link_NAG-ASN : bond 0.00583 ( 33) link_NAG-ASN : angle 3.32154 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 221 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 TYR cc_start: 0.6233 (m-80) cc_final: 0.6022 (m-80) REVERT: B 247 GLN cc_start: 0.7857 (tp40) cc_final: 0.7580 (tp40) REVERT: C 194 MET cc_start: 0.8284 (tpp) cc_final: 0.7888 (tpt) REVERT: b 321 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.6563 (mp-120) REVERT: b 357 ASP cc_start: 0.8479 (t0) cc_final: 0.8260 (t70) REVERT: b 371 TYR cc_start: 0.8793 (p90) cc_final: 0.8224 (p90) REVERT: c 351 MET cc_start: 0.8868 (tpt) cc_final: 0.8239 (tpp) REVERT: c 353 ASN cc_start: 0.7958 (m110) cc_final: 0.7530 (m110) outliers start: 30 outliers final: 22 residues processed: 232 average time/residue: 0.0931 time to fit residues: 31.0894 Evaluate side-chains 229 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain a residue 285 LEU Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 342 ASN Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 397 THR Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 348 GLN Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 395 ASN Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 91 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 ASN B 232 GLN ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 335 GLN ** b 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 354 HIS ** 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 = 0.4260 r_free = 0.4260 target = 0.192285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.162979 restraints weight = 13383.140| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.99 r_work: 0.3838 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10271 Z= 0.238 Angle : 0.827 12.150 14051 Z= 0.370 Chirality : 0.047 0.377 1757 Planarity : 0.004 0.043 1685 Dihedral : 7.991 57.325 2507 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.96 % Allowed : 15.62 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.27), residues: 971 helix: 0.75 (0.29), residues: 328 sheet: -2.14 (0.39), residues: 151 loop : -0.92 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG c 325 TYR 0.018 0.002 TYR c 363 PHE 0.015 0.002 PHE a 309 TRP 0.030 0.002 TRP A 196 HIS 0.007 0.001 HIS b 354 Details of bonding type rmsd covalent geometry : bond 0.00547 (10192) covalent geometry : angle 0.74669 (13835) SS BOND : bond 0.00507 ( 21) SS BOND : angle 1.39866 ( 42) hydrogen bonds : bond 0.03575 ( 356) hydrogen bonds : angle 4.95920 ( 945) link_ALPHA1-2 : bond 0.00829 ( 1) link_ALPHA1-2 : angle 2.17059 ( 3) link_ALPHA1-3 : bond 0.00099 ( 1) link_ALPHA1-3 : angle 5.47134 ( 3) link_ALPHA1-6 : bond 0.01362 ( 1) link_ALPHA1-6 : angle 1.34681 ( 3) link_BETA1-4 : bond 0.01014 ( 20) link_BETA1-4 : angle 3.08171 ( 60) link_BETA1-6 : bond 0.00240 ( 2) link_BETA1-6 : angle 1.51725 ( 6) link_NAG-ASN : bond 0.00621 ( 33) link_NAG-ASN : angle 3.34954 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ILE cc_start: 0.8995 (mm) cc_final: 0.8781 (pt) REVERT: B 120 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8235 (tt) REVERT: C 194 MET cc_start: 0.8389 (tpp) cc_final: 0.7924 (tpt) REVERT: a 379 ARG cc_start: 0.7240 (ttp80) cc_final: 0.7021 (ttp80) REVERT: b 321 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.6634 (mp-120) REVERT: b 371 TYR cc_start: 0.8858 (p90) cc_final: 0.8238 (p90) outliers start: 36 outliers final: 26 residues processed: 224 average time/residue: 0.0917 time to fit residues: 29.5667 Evaluate side-chains 226 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 342 ASN Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 397 THR Chi-restraints excluded: chain c residue 261 THR Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 336 LEU Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 395 ASN Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 118 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 109 optimal weight: 0.1980 chunk 75 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 348 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.196080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.167092 restraints weight = 13520.657| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 3.01 r_work: 0.3902 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10271 Z= 0.140 Angle : 0.729 11.374 14051 Z= 0.326 Chirality : 0.043 0.360 1757 Planarity : 0.004 0.043 1685 Dihedral : 7.596 55.656 2507 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.40 % Allowed : 16.61 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.27), residues: 971 helix: 0.89 (0.29), residues: 328 sheet: -1.96 (0.38), residues: 157 loop : -0.89 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG c 325 TYR 0.031 0.001 TYR c 363 PHE 0.010 0.001 PHE c 318 TRP 0.028 0.001 TRP A 196 HIS 0.004 0.001 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00307 (10192) covalent geometry : angle 0.65041 (13835) SS BOND : bond 0.00393 ( 21) SS BOND : angle 1.15188 ( 42) hydrogen bonds : bond 0.03090 ( 356) hydrogen bonds : angle 4.67710 ( 945) link_ALPHA1-2 : bond 0.01017 ( 1) link_ALPHA1-2 : angle 2.06931 ( 3) link_ALPHA1-3 : bond 0.00193 ( 1) link_ALPHA1-3 : angle 5.52333 ( 3) link_ALPHA1-6 : bond 0.01110 ( 1) link_ALPHA1-6 : angle 1.39134 ( 3) link_BETA1-4 : bond 0.01047 ( 20) link_BETA1-4 : angle 3.00043 ( 60) link_BETA1-6 : bond 0.00345 ( 2) link_BETA1-6 : angle 1.36224 ( 6) link_NAG-ASN : bond 0.00503 ( 33) link_NAG-ASN : angle 3.02606 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 215 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TYR cc_start: 0.6312 (m-80) cc_final: 0.6038 (m-80) REVERT: A 235 ARG cc_start: 0.8087 (ptp90) cc_final: 0.7710 (ptt180) REVERT: C 194 MET cc_start: 0.8357 (tpp) cc_final: 0.7971 (tpt) REVERT: a 338 ASN cc_start: 0.8840 (t0) cc_final: 0.8580 (t0) REVERT: b 321 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.6400 (mp-120) REVERT: b 357 ASP cc_start: 0.8377 (t0) cc_final: 0.8098 (t70) REVERT: b 371 TYR cc_start: 0.8822 (p90) cc_final: 0.8178 (p90) REVERT: c 351 MET cc_start: 0.8834 (tpt) cc_final: 0.8370 (tpp) REVERT: c 353 ASN cc_start: 0.7967 (m110) cc_final: 0.7547 (m110) outliers start: 40 outliers final: 27 residues processed: 234 average time/residue: 0.0940 time to fit residues: 31.6527 Evaluate side-chains 232 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain a residue 285 LEU Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 342 ASN Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 395 ASN Chi-restraints excluded: chain c residue 261 THR Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 348 GLN Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 395 ASN Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 118 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 105 optimal weight: 0.1980 chunk 100 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.196494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.167249 restraints weight = 13422.336| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 3.04 r_work: 0.3885 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10271 Z= 0.140 Angle : 0.730 10.808 14051 Z= 0.326 Chirality : 0.043 0.354 1757 Planarity : 0.004 0.040 1685 Dihedral : 7.436 56.210 2507 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.29 % Allowed : 16.50 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.27), residues: 971 helix: 0.98 (0.29), residues: 328 sheet: -1.84 (0.39), residues: 157 loop : -0.86 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 325 TYR 0.024 0.001 TYR c 363 PHE 0.011 0.001 PHE C 233 TRP 0.032 0.001 TRP A 196 HIS 0.005 0.001 HIS b 354 Details of bonding type rmsd covalent geometry : bond 0.00308 (10192) covalent geometry : angle 0.65397 (13835) SS BOND : bond 0.00377 ( 21) SS BOND : angle 1.15615 ( 42) hydrogen bonds : bond 0.03030 ( 356) hydrogen bonds : angle 4.58466 ( 945) link_ALPHA1-2 : bond 0.00986 ( 1) link_ALPHA1-2 : angle 2.04773 ( 3) link_ALPHA1-3 : bond 0.00221 ( 1) link_ALPHA1-3 : angle 5.44810 ( 3) link_ALPHA1-6 : bond 0.01088 ( 1) link_ALPHA1-6 : angle 1.40815 ( 3) link_BETA1-4 : bond 0.01064 ( 20) link_BETA1-4 : angle 2.98980 ( 60) link_BETA1-6 : bond 0.00381 ( 2) link_BETA1-6 : angle 1.29232 ( 6) link_NAG-ASN : bond 0.00495 ( 33) link_NAG-ASN : angle 2.96094 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TYR cc_start: 0.6348 (m-80) cc_final: 0.6038 (m-80) REVERT: A 235 ARG cc_start: 0.8095 (ptp90) cc_final: 0.7718 (ptt180) REVERT: C 194 MET cc_start: 0.8376 (tpp) cc_final: 0.7964 (tpt) REVERT: b 321 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.6342 (mp-120) REVERT: b 371 TYR cc_start: 0.8829 (p90) cc_final: 0.8133 (p90) REVERT: c 351 MET cc_start: 0.8842 (tpt) cc_final: 0.8242 (tpp) REVERT: c 410 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6795 (ttt) outliers start: 39 outliers final: 27 residues processed: 227 average time/residue: 0.0949 time to fit residues: 31.2254 Evaluate side-chains 226 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain a residue 285 LEU Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain b residue 262 PHE Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 342 ASN Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 395 ASN Chi-restraints excluded: chain c residue 261 THR Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 395 ASN Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 106 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.196275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.167091 restraints weight = 13418.235| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 3.04 r_work: 0.3888 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10271 Z= 0.148 Angle : 0.734 12.369 14051 Z= 0.328 Chirality : 0.043 0.345 1757 Planarity : 0.003 0.041 1685 Dihedral : 7.320 56.355 2507 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.07 % Allowed : 17.49 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.27), residues: 971 helix: 0.98 (0.29), residues: 331 sheet: -1.77 (0.39), residues: 157 loop : -0.95 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 282 TYR 0.022 0.001 TYR c 363 PHE 0.011 0.001 PHE b 316 TRP 0.030 0.001 TRP A 196 HIS 0.007 0.001 HIS b 354 Details of bonding type rmsd covalent geometry : bond 0.00333 (10192) covalent geometry : angle 0.66104 (13835) SS BOND : bond 0.00377 ( 21) SS BOND : angle 1.13732 ( 42) hydrogen bonds : bond 0.03022 ( 356) hydrogen bonds : angle 4.51809 ( 945) link_ALPHA1-2 : bond 0.00954 ( 1) link_ALPHA1-2 : angle 2.03696 ( 3) link_ALPHA1-3 : bond 0.00234 ( 1) link_ALPHA1-3 : angle 5.37225 ( 3) link_ALPHA1-6 : bond 0.00949 ( 1) link_ALPHA1-6 : angle 1.41962 ( 3) link_BETA1-4 : bond 0.01032 ( 20) link_BETA1-4 : angle 2.98699 ( 60) link_BETA1-6 : bond 0.00367 ( 2) link_BETA1-6 : angle 1.30505 ( 6) link_NAG-ASN : bond 0.00476 ( 33) link_NAG-ASN : angle 2.87933 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TYR cc_start: 0.6367 (m-80) cc_final: 0.6084 (m-80) REVERT: A 235 ARG cc_start: 0.8086 (ptp90) cc_final: 0.7755 (ptt180) REVERT: A 239 ILE cc_start: 0.8951 (mm) cc_final: 0.8609 (pt) REVERT: B 76 GLU cc_start: 0.8115 (tp30) cc_final: 0.7782 (tp30) REVERT: C 194 MET cc_start: 0.8427 (tpp) cc_final: 0.8032 (tpt) REVERT: a 338 ASN cc_start: 0.8853 (t0) cc_final: 0.8493 (t0) REVERT: b 321 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.6412 (mp-120) REVERT: b 371 TYR cc_start: 0.8827 (p90) cc_final: 0.8095 (p90) REVERT: c 351 MET cc_start: 0.8811 (tpt) cc_final: 0.8220 (tpp) REVERT: c 410 MET cc_start: 0.7028 (OUTLIER) cc_final: 0.6812 (ttt) outliers start: 37 outliers final: 29 residues processed: 225 average time/residue: 0.0992 time to fit residues: 32.1384 Evaluate side-chains 230 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain a residue 285 LEU Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain b residue 262 PHE Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 342 ASN Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 395 ASN Chi-restraints excluded: chain c residue 261 THR Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 395 ASN Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 41 optimal weight: 3.9990 chunk 85 optimal weight: 0.0970 chunk 57 optimal weight: 10.0000 chunk 11 optimal weight: 0.0060 chunk 3 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 GLN ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.199191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.170308 restraints weight = 13344.358| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 3.04 r_work: 0.3924 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10271 Z= 0.120 Angle : 0.707 10.338 14051 Z= 0.317 Chirality : 0.042 0.324 1757 Planarity : 0.003 0.043 1685 Dihedral : 7.068 55.793 2507 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.96 % Allowed : 17.82 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.27), residues: 971 helix: 1.05 (0.29), residues: 331 sheet: -1.67 (0.40), residues: 157 loop : -0.93 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 325 TYR 0.031 0.001 TYR c 363 PHE 0.012 0.001 PHE C 233 TRP 0.037 0.001 TRP A 196 HIS 0.005 0.001 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00262 (10192) covalent geometry : angle 0.63668 (13835) SS BOND : bond 0.00360 ( 21) SS BOND : angle 1.01350 ( 42) hydrogen bonds : bond 0.02843 ( 356) hydrogen bonds : angle 4.39851 ( 945) link_ALPHA1-2 : bond 0.00981 ( 1) link_ALPHA1-2 : angle 1.93689 ( 3) link_ALPHA1-3 : bond 0.00406 ( 1) link_ALPHA1-3 : angle 5.24715 ( 3) link_ALPHA1-6 : bond 0.00893 ( 1) link_ALPHA1-6 : angle 1.43316 ( 3) link_BETA1-4 : bond 0.01020 ( 20) link_BETA1-4 : angle 2.93610 ( 60) link_BETA1-6 : bond 0.00438 ( 2) link_BETA1-6 : angle 1.21940 ( 6) link_NAG-ASN : bond 0.00456 ( 33) link_NAG-ASN : angle 2.74950 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TYR cc_start: 0.6389 (m-80) cc_final: 0.6084 (m-80) REVERT: A 235 ARG cc_start: 0.8054 (ptp90) cc_final: 0.7695 (ptt180) REVERT: B 76 GLU cc_start: 0.8143 (tp30) cc_final: 0.7768 (tp30) REVERT: C 194 MET cc_start: 0.8407 (tpp) cc_final: 0.8005 (tpt) REVERT: a 324 GLN cc_start: 0.8224 (mp10) cc_final: 0.7927 (mp10) REVERT: a 338 ASN cc_start: 0.8839 (t0) cc_final: 0.8453 (t0) REVERT: a 398 HIS cc_start: 0.7964 (t70) cc_final: 0.7578 (t70) REVERT: b 321 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.6268 (mp-120) REVERT: b 371 TYR cc_start: 0.8807 (p90) cc_final: 0.8080 (p90) REVERT: c 351 MET cc_start: 0.8724 (tpt) cc_final: 0.8148 (tpp) REVERT: c 410 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6757 (ttt) outliers start: 36 outliers final: 29 residues processed: 223 average time/residue: 0.1025 time to fit residues: 32.8241 Evaluate side-chains 229 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain a residue 285 LEU Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain b residue 262 PHE Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 342 ASN Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 395 ASN Chi-restraints excluded: chain c residue 261 THR Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 395 ASN Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 97 optimal weight: 0.6980 chunk 33 optimal weight: 0.0020 chunk 70 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 14 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 55 optimal weight: 0.3980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 GLN ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.199532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.170957 restraints weight = 13290.980| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 3.02 r_work: 0.3929 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10271 Z= 0.123 Angle : 0.708 10.059 14051 Z= 0.320 Chirality : 0.042 0.317 1757 Planarity : 0.003 0.051 1685 Dihedral : 6.944 56.219 2507 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.63 % Allowed : 18.48 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.28), residues: 971 helix: 1.07 (0.29), residues: 331 sheet: -1.59 (0.40), residues: 157 loop : -0.88 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 193 TYR 0.029 0.001 TYR c 363 PHE 0.012 0.001 PHE C 233 TRP 0.035 0.001 TRP A 196 HIS 0.005 0.001 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00272 (10192) covalent geometry : angle 0.64114 (13835) SS BOND : bond 0.00351 ( 21) SS BOND : angle 1.01181 ( 42) hydrogen bonds : bond 0.02889 ( 356) hydrogen bonds : angle 4.37197 ( 945) link_ALPHA1-2 : bond 0.00920 ( 1) link_ALPHA1-2 : angle 1.91780 ( 3) link_ALPHA1-3 : bond 0.00451 ( 1) link_ALPHA1-3 : angle 5.09804 ( 3) link_ALPHA1-6 : bond 0.00701 ( 1) link_ALPHA1-6 : angle 1.40712 ( 3) link_BETA1-4 : bond 0.01014 ( 20) link_BETA1-4 : angle 2.91906 ( 60) link_BETA1-6 : bond 0.00433 ( 2) link_BETA1-6 : angle 1.20903 ( 6) link_NAG-ASN : bond 0.00432 ( 33) link_NAG-ASN : angle 2.67038 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TYR cc_start: 0.6368 (m-80) cc_final: 0.6057 (m-80) REVERT: A 235 ARG cc_start: 0.8014 (ptp90) cc_final: 0.7687 (ptt180) REVERT: B 76 GLU cc_start: 0.8161 (tp30) cc_final: 0.7798 (tp30) REVERT: C 194 MET cc_start: 0.8403 (tpp) cc_final: 0.8051 (tpt) REVERT: a 324 GLN cc_start: 0.8230 (mp10) cc_final: 0.7915 (mp10) REVERT: a 338 ASN cc_start: 0.8833 (t0) cc_final: 0.8438 (t0) REVERT: a 398 HIS cc_start: 0.7947 (t70) cc_final: 0.7388 (t70) REVERT: b 371 TYR cc_start: 0.8822 (p90) cc_final: 0.8104 (p90) REVERT: c 351 MET cc_start: 0.8676 (tpt) cc_final: 0.8116 (tpp) outliers start: 33 outliers final: 29 residues processed: 216 average time/residue: 0.0928 time to fit residues: 29.0804 Evaluate side-chains 225 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain a residue 285 LEU Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain b residue 262 PHE Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 285 LEU Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 342 ASN Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 395 ASN Chi-restraints excluded: chain c residue 261 THR Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 295 ASN Chi-restraints excluded: chain c residue 333 SER Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 395 ASN Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 79 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 87 optimal weight: 0.0270 chunk 20 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 109 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.199426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.170428 restraints weight = 13408.969| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 3.05 r_work: 0.3923 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10271 Z= 0.130 Angle : 0.708 9.722 14051 Z= 0.320 Chirality : 0.042 0.341 1757 Planarity : 0.004 0.059 1685 Dihedral : 6.931 56.288 2507 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.52 % Allowed : 18.70 % Favored : 77.78 % 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 aren not related in a simple way. whole: -0.52 (0.28), residues: 971 helix: 1.10 (0.29), residues: 331 sheet: -1.59 (0.40), residues: 157 loop : -0.88 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 282 TYR 0.028 0.001 TYR c 363 PHE 0.012 0.001 PHE C 233 TRP 0.035 0.001 TRP A 196 HIS 0.006 0.001 HIS b 354 Details of bonding type rmsd covalent geometry : bond 0.00291 (10192) covalent geometry : angle 0.64072 (13835) SS BOND : bond 0.00358 ( 21) SS BOND : angle 1.01089 ( 42) hydrogen bonds : bond 0.02890 ( 356) hydrogen bonds : angle 4.35115 ( 945) link_ALPHA1-2 : bond 0.00865 ( 1) link_ALPHA1-2 : angle 1.91589 ( 3) link_ALPHA1-3 : bond 0.00437 ( 1) link_ALPHA1-3 : angle 4.99295 ( 3) link_ALPHA1-6 : bond 0.00757 ( 1) link_ALPHA1-6 : angle 1.40285 ( 3) link_BETA1-4 : bond 0.01016 ( 20) link_BETA1-4 : angle 2.91043 ( 60) link_BETA1-6 : bond 0.00414 ( 2) link_BETA1-6 : angle 1.22364 ( 6) link_NAG-ASN : bond 0.00460 ( 33) link_NAG-ASN : angle 2.66706 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2199.64 seconds wall clock time: 38 minutes 48.81 seconds (2328.81 seconds total)