Starting phenix.real_space_refine on Wed Sep 17 17:17:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ck8_45644/09_2025/9ck8_45644.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ck8_45644/09_2025/9ck8_45644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ck8_45644/09_2025/9ck8_45644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ck8_45644/09_2025/9ck8_45644.map" model { file = "/net/cci-nas-00/data/ceres_data/9ck8_45644/09_2025/9ck8_45644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ck8_45644/09_2025/9ck8_45644.cif" } resolution = 3.04 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 6211 2.51 5 N 1640 2.21 5 O 2028 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: 9966 Number of models: 1 Model: "" Number of chains: 30 Chain: "H" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 590 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'TRANS': 117} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 118 Planarities with less than four sites: {'UNK:plan-1': 118} Unresolved non-hydrogen planarities: 118 Chain: "L" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 530 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'TRANS': 105} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 106 Planarities with less than four sites: {'UNK:plan-1': 106} Unresolved non-hydrogen planarities: 106 Chain: "C" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1498 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 2 Chain: "A" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1498 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 2 Chain: "B" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1494 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 182} Chain breaks: 2 Chain: "a" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1193 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain breaks: 1 Chain: "b" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1177 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain breaks: 1 Chain: "c" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1193 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 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: "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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 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: 2.67, per 1000 atoms: 0.27 Number of scatterers: 9966 At special positions: 0 Unit cell: (119.188, 89.032, 91.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 2028 8.00 N 1640 7.00 C 6211 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.03 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 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.02 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 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=2.02 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN M 4 " - " MAN M 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA T 3 " - " MAN T 4 " ALPHA1-6 " BMA M 3 " - " MAN M 6 " " BMA T 3 " - " MAN T 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " 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 T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " BETA1-6 " NAG F 1 " - " FUC F 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG K 1 " - " FUC K 3 " " NAG O 1 " - " FUC O 3 " NAG-ASN " NAG A 301 " - " ASN A 109 " " NAG A 302 " - " ASN A 224 " " NAG A 303 " - " ASN A 89 " " NAG B 301 " - " ASN B 99 " " NAG B 302 " - " ASN B 109 " " NAG C 301 " - " ASN C 89 " " NAG C 302 " - " ASN C 99 " " NAG C 303 " - " ASN C 109 " " NAG C 304 " - " ASN C 224 " " NAG D 1 " - " ASN C 167 " " NAG E 1 " - " ASN C 79 " " NAG F 1 " - " ASN C 119 " " NAG G 1 " - " ASN A 99 " " NAG I 1 " - " ASN A 167 " " NAG J 1 " - " ASN A 79 " " NAG K 1 " - " ASN A 119 " " NAG M 1 " - " ASN B 79 " " NAG N 1 " - " ASN B 89 " " NAG O 1 " - " ASN B 119 " " NAG P 1 " - " ASN B 167 " " NAG Q 1 " - " ASN B 224 " " NAG R 1 " - " ASN a 373 " " NAG S 1 " - " ASN a 365 " " NAG T 1 " - " ASN b 365 " " NAG U 1 " - " ASN c 365 " " NAG a 701 " - " ASN a 395 " " NAG a 702 " - " ASN a 390 " " NAG b 701 " - " ASN b 373 " " NAG b 702 " - " ASN b 395 " " NAG b 703 " - " ASN b 390 " " NAG c 701 " - " ASN c 373 " " NAG c 702 " - " ASN c 395 " " NAG c 703 " - " ASN c 390 " Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 369.7 milliseconds Enol-peptide restraints added in 238.4 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: 2342 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 15 sheets defined 40.0% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'H' and resid 70 through 73 Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.774A pdb=" N THR C 77 " --> pdb=" O ASN C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.608A pdb=" N GLY C 160 " --> pdb=" O PHE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 195 Processing helix chain 'C' and resid 238 through 245 Processing helix chain 'C' and resid 246 through 248 No H-bonds generated for 'chain 'C' and resid 246 through 248' Processing helix chain 'A' and resid 74 through 79 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: 3.505A pdb=" N ARG A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'B' and resid 76 through 81 removed outlier: 3.554A pdb=" N ASN B 79 " --> pdb=" O GLU B 76 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N MET B 80 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.986A pdb=" N ALA B 123 " --> pdb=" O ASN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.732A pdb=" N GLY B 160 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 Processing helix chain 'B' and resid 238 through 246 removed outlier: 4.090A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'a' and resid 281 through 285 Processing helix chain 'a' and resid 294 through 304 removed outlier: 3.784A pdb=" N LYS a 300 " --> pdb=" O THR a 296 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS a 301 " --> pdb=" O ALA a 297 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN a 302 " --> pdb=" O VAL a 298 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU a 303 " --> pdb=" O ALA a 299 " (cutoff:3.500A) Processing helix chain 'a' and resid 307 through 326 removed outlier: 3.614A pdb=" N ASP a 311 " --> pdb=" O GLU a 307 " (cutoff:3.500A) Processing helix chain 'a' and resid 334 through 345 removed outlier: 5.489A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ALA a 343 " --> pdb=" O LYS a 339 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.689A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 399 through 412 Processing helix chain 'b' and resid 294 through 300 removed outlier: 3.781A pdb=" N LYS b 300 " --> pdb=" O THR b 296 " (cutoff:3.500A) Processing helix chain 'b' and resid 301 through 303 No H-bonds generated for 'chain 'b' and resid 301 through 303' Processing helix chain 'b' and resid 307 through 326 removed outlier: 3.552A pdb=" N ASP b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) Processing helix chain 'b' and resid 334 through 345 removed outlier: 5.541A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.789A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 399 through 413 Processing helix chain 'c' and resid 294 through 304 removed outlier: 3.840A pdb=" N LYS c 300 " --> pdb=" O THR c 296 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N CYS c 301 " --> pdb=" O ALA c 297 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASN c 302 " --> pdb=" O VAL c 298 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU c 303 " --> pdb=" O ALA c 299 " (cutoff:3.500A) Processing helix chain 'c' and resid 307 through 325 Processing helix chain 'c' and resid 334 through 345 removed outlier: 5.887A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.565A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 399 through 413 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.650A pdb=" N UNK H 5 " --> pdb=" O UNK H 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.834A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N UNK H 50 " --> pdb=" O UNK H 35 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N UNK H 35 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N UNK H 52 " --> pdb=" O UNK H 33 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N UNK H 33 " --> pdb=" O UNK H 52 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N UNK H 92 " --> pdb=" O UNK H 103 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N UNK H 103 " --> pdb=" O UNK H 92 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N UNK H 94 " --> pdb=" O UNK H 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA4, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.744A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (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 153 through 155 removed outlier: 4.096A pdb=" N THR C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR C 94 " --> pdb=" O CYS C 86 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET C 96 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N THR C 87 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ARG C 235 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 61 through 62 removed outlier: 3.582A pdb=" N TYR A 66 " --> pdb=" O TYR A 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 84 through 89 removed outlier: 6.556A pdb=" N HIS A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AB1, first strand: chain 'B' and resid 153 through 156 removed outlier: 6.574A pdb=" N HIS B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N THR B 87 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ARG B 235 " --> pdb=" O THR B 87 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 278 through 280 Processing sheet with id=AB3, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AB4, first strand: chain 'b' and resid 279 through 280 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 278 through 280 396 hydrogen bonds defined for protein. 1062 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: 1.90 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3061 1.34 - 1.46: 2453 1.46 - 1.58: 4489 1.58 - 1.70: 0 1.70 - 1.83: 132 Bond restraints: 10135 Sorted by residual: bond pdb=" N ILE b 345 " pdb=" CA ILE b 345 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.14e-02 7.69e+03 1.13e+01 bond pdb=" N THR B 101 " pdb=" CA THR B 101 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.29e-02 6.01e+03 8.55e+00 bond pdb=" CA SER A 154 " pdb=" CB SER A 154 " ideal model delta sigma weight residual 1.533 1.485 0.048 1.69e-02 3.50e+03 8.23e+00 bond pdb=" N ASN A 89 " pdb=" CA ASN A 89 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.16e-02 7.43e+03 7.69e+00 bond pdb=" N GLY B 98 " pdb=" CA GLY B 98 " ideal model delta sigma weight residual 1.447 1.474 -0.027 1.01e-02 9.80e+03 7.33e+00 ... (remaining 10130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 13145 2.02 - 4.05: 539 4.05 - 6.07: 68 6.07 - 8.09: 9 8.09 - 10.11: 1 Bond angle restraints: 13762 Sorted by residual: angle pdb=" CA GLY B 102 " pdb=" C GLY B 102 " pdb=" O GLY B 102 " ideal model delta sigma weight residual 121.61 117.63 3.98 1.05e+00 9.07e-01 1.43e+01 angle pdb=" CB ASN a 390 " pdb=" CG ASN a 390 " pdb=" ND2 ASN a 390 " ideal model delta sigma weight residual 116.40 122.08 -5.68 1.50e+00 4.44e-01 1.43e+01 angle pdb=" CA ASN A 119 " pdb=" C ASN A 119 " pdb=" O ASN A 119 " ideal model delta sigma weight residual 122.64 117.97 4.67 1.25e+00 6.40e-01 1.39e+01 angle pdb=" N ASN b 365 " pdb=" CA ASN b 365 " pdb=" C ASN b 365 " ideal model delta sigma weight residual 113.17 108.54 4.63 1.26e+00 6.30e-01 1.35e+01 angle pdb=" CA LEU b 344 " pdb=" C LEU b 344 " pdb=" O LEU b 344 " ideal model delta sigma weight residual 120.42 116.55 3.87 1.06e+00 8.90e-01 1.33e+01 ... (remaining 13757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.58: 6496 21.58 - 43.15: 227 43.15 - 64.73: 54 64.73 - 86.31: 27 86.31 - 107.88: 9 Dihedral angle restraints: 6813 sinusoidal: 3212 harmonic: 3601 Sorted by residual: dihedral pdb=" CB CYS A 86 " pdb=" SG CYS A 86 " pdb=" SG CYS A 231 " pdb=" CB CYS A 231 " ideal model delta sinusoidal sigma weight residual -86.00 -174.04 88.04 1 1.00e+01 1.00e-02 9.27e+01 dihedral pdb=" CB CYS B 207 " pdb=" SG CYS B 207 " pdb=" SG CYS b 360 " pdb=" CB CYS b 360 " ideal model delta sinusoidal sigma weight residual 93.00 164.18 -71.18 1 1.00e+01 1.00e-02 6.50e+01 dihedral pdb=" CB CYS C 86 " pdb=" SG CYS C 86 " pdb=" SG CYS C 231 " pdb=" CB CYS C 231 " ideal model delta sinusoidal sigma weight residual -86.00 -156.77 70.77 1 1.00e+01 1.00e-02 6.44e+01 ... (remaining 6810 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 1717 0.147 - 0.294: 23 0.294 - 0.441: 4 0.441 - 0.588: 3 0.588 - 0.734: 1 Chirality restraints: 1748 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-02 2.50e+03 4.70e+02 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.34e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.22e+01 ... (remaining 1745 not shown) Planarity restraints: 1709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 703 " -0.311 2.00e-02 2.50e+03 2.65e-01 8.77e+02 pdb=" C7 NAG c 703 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG c 703 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG c 703 " 0.461 2.00e-02 2.50e+03 pdb=" O7 NAG c 703 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 2 " 0.272 2.00e-02 2.50e+03 2.27e-01 6.46e+02 pdb=" C7 NAG Q 2 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG Q 2 " 0.182 2.00e-02 2.50e+03 pdb=" N2 NAG Q 2 " -0.382 2.00e-02 2.50e+03 pdb=" O7 NAG Q 2 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 702 " -0.260 2.00e-02 2.50e+03 2.18e-01 5.93e+02 pdb=" C7 NAG c 702 " 0.069 2.00e-02 2.50e+03 pdb=" C8 NAG c 702 " -0.174 2.00e-02 2.50e+03 pdb=" N2 NAG c 702 " 0.367 2.00e-02 2.50e+03 pdb=" O7 NAG c 702 " -0.002 2.00e-02 2.50e+03 ... (remaining 1706 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 192 2.68 - 3.23: 9469 3.23 - 3.79: 14683 3.79 - 4.34: 20738 4.34 - 4.90: 33657 Nonbonded interactions: 78739 Sorted by model distance: nonbonded pdb=" O ALA B 195 " pdb=" OG SER B 199 " model vdw 2.121 3.040 nonbonded pdb=" OE1 GLN B 218 " pdb=" O6 NAG B 302 " model vdw 2.212 3.040 nonbonded pdb=" O ALA A 195 " pdb=" OG SER A 199 " model vdw 2.239 3.040 nonbonded pdb=" O THR C 77 " pdb=" O6 NAG E 1 " model vdw 2.250 3.040 nonbonded pdb=" OH TYR a 371 " pdb=" O7 NAG R 1 " model vdw 2.294 3.040 ... (remaining 78734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 60 through 202 or resid 207 through 302)) selection = chain 'B' selection = (chain 'C' and (resid 60 through 202 or resid 207 through 302)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'O' } ncs_group { reference = (chain 'H' and resid 14 through 108) 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 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: 12.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.470 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 : 0.006 0.131 10215 Z= 0.290 Angle : 1.005 15.275 13981 Z= 0.487 Chirality : 0.055 0.734 1748 Planarity : 0.014 0.265 1676 Dihedral : 12.903 107.885 4408 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.26), residues: 971 helix: 0.17 (0.28), residues: 327 sheet: -0.55 (0.43), residues: 130 loop : -0.53 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 193 TYR 0.023 0.002 TYR C 253 PHE 0.014 0.002 PHE a 399 TRP 0.011 0.001 TRP A 227 HIS 0.010 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00544 (10135) covalent geometry : angle 0.88683 (13762) SS BOND : bond 0.00415 ( 21) SS BOND : angle 1.05194 ( 42) hydrogen bonds : bond 0.15810 ( 396) hydrogen bonds : angle 6.36840 ( 1062) link_ALPHA1-2 : bond 0.00017 ( 1) link_ALPHA1-2 : angle 1.27520 ( 3) link_ALPHA1-3 : bond 0.00292 ( 2) link_ALPHA1-3 : angle 1.25703 ( 6) link_ALPHA1-6 : bond 0.00553 ( 2) link_ALPHA1-6 : angle 1.58988 ( 6) link_BETA1-4 : bond 0.00497 ( 18) link_BETA1-4 : angle 2.00528 ( 54) link_BETA1-6 : bond 0.00426 ( 3) link_BETA1-6 : angle 2.85187 ( 9) link_NAG-ASN : bond 0.02638 ( 33) link_NAG-ASN : angle 5.45196 ( 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 188 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 SER cc_start: 0.8731 (p) cc_final: 0.8433 (t) REVERT: C 192 MET cc_start: 0.7809 (mtm) cc_final: 0.7499 (mmt) REVERT: B 214 MET cc_start: 0.8027 (ptm) cc_final: 0.7732 (mtt) REVERT: a 307 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7587 (mm-30) REVERT: b 298 VAL cc_start: 0.8668 (m) cc_final: 0.8450 (t) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1153 time to fit residues: 29.3211 Evaluate side-chains 161 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN A 149 GLN A 179 HIS A 218 GLN B 158 ASN B 218 GLN B 247 GLN a 295 ASN a 302 ASN b 324 GLN b 346 ASN b 354 HIS b 374 HIS b 409 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.181383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.155292 restraints weight = 11526.357| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.14 r_work: 0.3659 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10215 Z= 0.175 Angle : 0.762 14.365 13981 Z= 0.338 Chirality : 0.050 0.592 1748 Planarity : 0.003 0.037 1676 Dihedral : 8.813 74.001 2508 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.33 % Allowed : 4.32 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.26), residues: 971 helix: 0.32 (0.29), residues: 339 sheet: -0.51 (0.46), residues: 120 loop : -0.43 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 193 TYR 0.012 0.001 TYR C 94 PHE 0.020 0.002 PHE C 157 TRP 0.009 0.001 TRP B 227 HIS 0.005 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00399 (10135) covalent geometry : angle 0.65287 (13762) SS BOND : bond 0.00439 ( 21) SS BOND : angle 0.87589 ( 42) hydrogen bonds : bond 0.03639 ( 396) hydrogen bonds : angle 4.89821 ( 1062) link_ALPHA1-2 : bond 0.01408 ( 1) link_ALPHA1-2 : angle 2.94154 ( 3) link_ALPHA1-3 : bond 0.00834 ( 2) link_ALPHA1-3 : angle 2.05027 ( 6) link_ALPHA1-6 : bond 0.00649 ( 2) link_ALPHA1-6 : angle 1.65627 ( 6) link_BETA1-4 : bond 0.00483 ( 18) link_BETA1-4 : angle 2.13629 ( 54) link_BETA1-6 : bond 0.00473 ( 3) link_BETA1-6 : angle 2.13853 ( 9) link_NAG-ASN : bond 0.00905 ( 33) link_NAG-ASN : angle 4.35010 ( 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 186 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 192 MET cc_start: 0.8265 (mtm) cc_final: 0.7735 (mmt) REVERT: B 214 MET cc_start: 0.8333 (ptm) cc_final: 0.7900 (mtt) REVERT: B 219 TYR cc_start: 0.8876 (m-80) cc_final: 0.8634 (m-80) REVERT: B 247 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.6657 (tm130) REVERT: a 307 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7972 (mm-30) REVERT: a 404 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7805 (mm-30) REVERT: b 409 ASN cc_start: 0.7737 (m110) cc_final: 0.7512 (m110) outliers start: 12 outliers final: 10 residues processed: 177 average time/residue: 0.1074 time to fit residues: 26.2627 Evaluate side-chains 175 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain b residue 320 LYS Chi-restraints excluded: chain c residue 265 THR Chi-restraints excluded: chain c residue 296 THR Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 43 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN B 247 GLN a 374 HIS c 353 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.178616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.151719 restraints weight = 11620.684| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.17 r_work: 0.3623 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10215 Z= 0.190 Angle : 0.722 14.299 13981 Z= 0.323 Chirality : 0.047 0.571 1748 Planarity : 0.003 0.050 1676 Dihedral : 8.515 68.005 2508 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.11 % Allowed : 5.32 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.26), residues: 971 helix: 0.32 (0.29), residues: 339 sheet: -0.51 (0.45), residues: 128 loop : -0.44 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 257 TYR 0.011 0.001 TYR C 62 PHE 0.014 0.001 PHE A 191 TRP 0.013 0.001 TRP C 227 HIS 0.005 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00445 (10135) covalent geometry : angle 0.61724 (13762) SS BOND : bond 0.00395 ( 21) SS BOND : angle 0.87109 ( 42) hydrogen bonds : bond 0.03444 ( 396) hydrogen bonds : angle 4.76511 ( 1062) link_ALPHA1-2 : bond 0.01201 ( 1) link_ALPHA1-2 : angle 2.43482 ( 3) link_ALPHA1-3 : bond 0.00743 ( 2) link_ALPHA1-3 : angle 1.81395 ( 6) link_ALPHA1-6 : bond 0.00394 ( 2) link_ALPHA1-6 : angle 1.67273 ( 6) link_BETA1-4 : bond 0.00374 ( 18) link_BETA1-4 : angle 2.01798 ( 54) link_BETA1-6 : bond 0.00464 ( 3) link_BETA1-6 : angle 2.33533 ( 9) link_NAG-ASN : bond 0.00732 ( 33) link_NAG-ASN : angle 4.12744 ( 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 188 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 192 MET cc_start: 0.8276 (mtm) cc_final: 0.7708 (mmt) REVERT: B 214 MET cc_start: 0.8356 (ptm) cc_final: 0.7869 (mtt) REVERT: B 247 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.6447 (tm130) REVERT: a 307 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7989 (mm-30) REVERT: a 404 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7808 (mm-30) REVERT: a 409 ASN cc_start: 0.8664 (m-40) cc_final: 0.8284 (m110) outliers start: 19 outliers final: 16 residues processed: 172 average time/residue: 0.1041 time to fit residues: 24.9849 Evaluate side-chains 181 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain b residue 320 LYS Chi-restraints excluded: chain b residue 332 MET Chi-restraints excluded: chain b residue 377 THR Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 402 ASP Chi-restraints excluded: chain c residue 265 THR Chi-restraints excluded: chain c residue 296 THR Chi-restraints excluded: chain c residue 304 LYS Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 10 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 GLN b 409 ASN c 354 HIS c 405 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.175785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.148746 restraints weight = 11700.993| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.18 r_work: 0.3592 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10215 Z= 0.214 Angle : 0.741 14.639 13981 Z= 0.332 Chirality : 0.048 0.575 1748 Planarity : 0.004 0.053 1676 Dihedral : 8.326 63.362 2508 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.44 % Allowed : 5.76 % Favored : 91.80 % 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: -0.32 (0.26), residues: 971 helix: 0.41 (0.29), residues: 331 sheet: -0.18 (0.46), residues: 124 loop : -0.56 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 248 TYR 0.012 0.001 TYR C 62 PHE 0.015 0.002 PHE A 191 TRP 0.015 0.001 TRP C 227 HIS 0.006 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00503 (10135) covalent geometry : angle 0.63993 (13762) SS BOND : bond 0.00439 ( 21) SS BOND : angle 0.92090 ( 42) hydrogen bonds : bond 0.03436 ( 396) hydrogen bonds : angle 4.76431 ( 1062) link_ALPHA1-2 : bond 0.01272 ( 1) link_ALPHA1-2 : angle 2.68492 ( 3) link_ALPHA1-3 : bond 0.00809 ( 2) link_ALPHA1-3 : angle 1.89413 ( 6) link_ALPHA1-6 : bond 0.00318 ( 2) link_ALPHA1-6 : angle 1.71252 ( 6) link_BETA1-4 : bond 0.00405 ( 18) link_BETA1-4 : angle 2.05074 ( 54) link_BETA1-6 : bond 0.00517 ( 3) link_BETA1-6 : angle 2.44028 ( 9) link_NAG-ASN : bond 0.00805 ( 33) link_NAG-ASN : angle 4.10264 ( 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 184 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 192 MET cc_start: 0.8227 (mtm) cc_final: 0.7682 (mmt) REVERT: B 214 MET cc_start: 0.8393 (ptm) cc_final: 0.7877 (mtt) REVERT: B 247 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.6424 (tm130) REVERT: a 307 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8049 (mm-30) REVERT: a 404 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7840 (mm-30) REVERT: a 409 ASN cc_start: 0.8685 (m-40) cc_final: 0.8388 (m110) outliers start: 22 outliers final: 17 residues processed: 168 average time/residue: 0.1059 time to fit residues: 24.3261 Evaluate side-chains 180 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain b residue 320 LYS Chi-restraints excluded: chain b residue 332 MET Chi-restraints excluded: chain b residue 377 THR Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 402 ASP Chi-restraints excluded: chain c residue 265 THR Chi-restraints excluded: chain c residue 296 THR Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 113 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 354 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.177420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.150598 restraints weight = 11660.572| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.19 r_work: 0.3615 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10215 Z= 0.148 Angle : 0.675 13.824 13981 Z= 0.300 Chirality : 0.045 0.550 1748 Planarity : 0.003 0.043 1676 Dihedral : 7.884 58.803 2508 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.77 % Allowed : 6.76 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.27), residues: 971 helix: 0.60 (0.29), residues: 331 sheet: -0.06 (0.48), residues: 122 loop : -0.57 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 248 TYR 0.011 0.001 TYR B 150 PHE 0.013 0.001 PHE A 191 TRP 0.014 0.001 TRP C 227 HIS 0.004 0.001 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00340 (10135) covalent geometry : angle 0.57332 (13762) SS BOND : bond 0.00334 ( 21) SS BOND : angle 0.78069 ( 42) hydrogen bonds : bond 0.03085 ( 396) hydrogen bonds : angle 4.56979 ( 1062) link_ALPHA1-2 : bond 0.01232 ( 1) link_ALPHA1-2 : angle 2.59769 ( 3) link_ALPHA1-3 : bond 0.00910 ( 2) link_ALPHA1-3 : angle 1.81553 ( 6) link_ALPHA1-6 : bond 0.00411 ( 2) link_ALPHA1-6 : angle 1.68877 ( 6) link_BETA1-4 : bond 0.00400 ( 18) link_BETA1-4 : angle 1.96043 ( 54) link_BETA1-6 : bond 0.00699 ( 3) link_BETA1-6 : angle 2.38091 ( 9) link_NAG-ASN : bond 0.00692 ( 33) link_NAG-ASN : angle 3.89349 ( 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 184 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 192 MET cc_start: 0.8200 (mtm) cc_final: 0.7665 (mmt) REVERT: B 214 MET cc_start: 0.8370 (ptm) cc_final: 0.7854 (mtt) REVERT: a 307 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8038 (mm-30) REVERT: a 404 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7833 (mm-30) REVERT: a 409 ASN cc_start: 0.8686 (m-40) cc_final: 0.8355 (m110) outliers start: 16 outliers final: 13 residues processed: 173 average time/residue: 0.1107 time to fit residues: 26.3107 Evaluate side-chains 179 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain b residue 332 MET Chi-restraints excluded: chain b residue 377 THR Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 402 ASP Chi-restraints excluded: chain c residue 265 THR Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 409 ASN c 354 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.178262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.151766 restraints weight = 11665.219| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.19 r_work: 0.3626 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10215 Z= 0.131 Angle : 0.649 13.424 13981 Z= 0.288 Chirality : 0.044 0.527 1748 Planarity : 0.003 0.040 1676 Dihedral : 7.599 56.712 2508 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.00 % Allowed : 7.21 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.27), residues: 971 helix: 0.72 (0.29), residues: 331 sheet: 0.07 (0.48), residues: 122 loop : -0.54 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG b 379 TYR 0.012 0.001 TYR B 150 PHE 0.012 0.001 PHE A 191 TRP 0.014 0.001 TRP C 227 HIS 0.003 0.001 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00296 (10135) covalent geometry : angle 0.54907 (13762) SS BOND : bond 0.00289 ( 21) SS BOND : angle 0.73323 ( 42) hydrogen bonds : bond 0.02950 ( 396) hydrogen bonds : angle 4.46304 ( 1062) link_ALPHA1-2 : bond 0.01262 ( 1) link_ALPHA1-2 : angle 2.52983 ( 3) link_ALPHA1-3 : bond 0.01019 ( 2) link_ALPHA1-3 : angle 1.85415 ( 6) link_ALPHA1-6 : bond 0.00417 ( 2) link_ALPHA1-6 : angle 1.61726 ( 6) link_BETA1-4 : bond 0.00394 ( 18) link_BETA1-4 : angle 1.91796 ( 54) link_BETA1-6 : bond 0.00709 ( 3) link_BETA1-6 : angle 2.35125 ( 9) link_NAG-ASN : bond 0.00669 ( 33) link_NAG-ASN : angle 3.77246 ( 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 187 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 192 MET cc_start: 0.8171 (mtm) cc_final: 0.7637 (mmt) REVERT: B 214 MET cc_start: 0.8372 (ptm) cc_final: 0.7846 (mtt) REVERT: B 247 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8565 (tp40) REVERT: a 307 GLU cc_start: 0.8266 (mm-30) cc_final: 0.8029 (mm-30) REVERT: a 404 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7788 (mm-30) REVERT: a 409 ASN cc_start: 0.8675 (m-40) cc_final: 0.8262 (m110) outliers start: 18 outliers final: 16 residues processed: 174 average time/residue: 0.1141 time to fit residues: 27.1221 Evaluate side-chains 185 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain b residue 332 MET Chi-restraints excluded: chain b residue 377 THR Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 402 ASP Chi-restraints excluded: chain c residue 265 THR Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 296 THR Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 58 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 112 optimal weight: 0.0170 chunk 77 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 overall best weight: 2.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS B 247 GLN a 409 ASN c 354 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.159233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.134290 restraints weight = 11819.211| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.02 r_work: 0.3224 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 10215 Z= 0.283 Angle : 0.809 15.383 13981 Z= 0.362 Chirality : 0.050 0.596 1748 Planarity : 0.004 0.059 1676 Dihedral : 8.238 55.629 2508 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.66 % Allowed : 8.09 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.42 (0.26), residues: 971 helix: 0.36 (0.29), residues: 331 sheet: 0.03 (0.46), residues: 124 loop : -0.72 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 379 TYR 0.014 0.002 TYR C 62 PHE 0.017 0.002 PHE A 191 TRP 0.018 0.002 TRP C 227 HIS 0.006 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00674 (10135) covalent geometry : angle 0.71606 (13762) SS BOND : bond 0.00554 ( 21) SS BOND : angle 1.02904 ( 42) hydrogen bonds : bond 0.03734 ( 396) hydrogen bonds : angle 4.89812 ( 1062) link_ALPHA1-2 : bond 0.01297 ( 1) link_ALPHA1-2 : angle 2.92245 ( 3) link_ALPHA1-3 : bond 0.00618 ( 2) link_ALPHA1-3 : angle 2.09445 ( 6) link_ALPHA1-6 : bond 0.00182 ( 2) link_ALPHA1-6 : angle 1.80132 ( 6) link_BETA1-4 : bond 0.00478 ( 18) link_BETA1-4 : angle 2.10241 ( 54) link_BETA1-6 : bond 0.00583 ( 3) link_BETA1-6 : angle 2.68249 ( 9) link_NAG-ASN : bond 0.00735 ( 33) link_NAG-ASN : angle 4.11396 ( 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 188 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 192 MET cc_start: 0.8115 (mtm) cc_final: 0.7360 (mmt) REVERT: B 214 MET cc_start: 0.8407 (ptm) cc_final: 0.7687 (mtt) REVERT: B 247 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8287 (tp40) REVERT: a 307 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7829 (mm-30) REVERT: a 404 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7780 (mm-30) REVERT: a 409 ASN cc_start: 0.8583 (m110) cc_final: 0.8190 (m110) REVERT: b 379 ARG cc_start: 0.7681 (ttp80) cc_final: 0.7450 (ttp80) REVERT: c 332 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.6463 (ttt) outliers start: 24 outliers final: 17 residues processed: 173 average time/residue: 0.1112 time to fit residues: 26.6897 Evaluate side-chains 179 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain b residue 377 THR Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 402 ASP Chi-restraints excluded: chain c residue 265 THR Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 296 THR Chi-restraints excluded: chain c residue 332 MET Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 2 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS B 247 GLN c 342 ASN c 354 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.159924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.134458 restraints weight = 11763.639| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.08 r_work: 0.3265 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10215 Z= 0.129 Angle : 0.670 13.791 13981 Z= 0.299 Chirality : 0.045 0.555 1748 Planarity : 0.003 0.038 1676 Dihedral : 7.766 59.480 2508 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.22 % Allowed : 8.76 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.26), residues: 971 helix: 0.60 (0.29), residues: 331 sheet: 0.05 (0.47), residues: 122 loop : -0.64 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 379 TYR 0.015 0.001 TYR B 150 PHE 0.011 0.001 PHE A 191 TRP 0.015 0.001 TRP C 227 HIS 0.003 0.001 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00288 (10135) covalent geometry : angle 0.57341 (13762) SS BOND : bond 0.00481 ( 21) SS BOND : angle 0.86222 ( 42) hydrogen bonds : bond 0.03041 ( 396) hydrogen bonds : angle 4.56434 ( 1062) link_ALPHA1-2 : bond 0.01332 ( 1) link_ALPHA1-2 : angle 2.64569 ( 3) link_ALPHA1-3 : bond 0.00931 ( 2) link_ALPHA1-3 : angle 1.74118 ( 6) link_ALPHA1-6 : bond 0.00418 ( 2) link_ALPHA1-6 : angle 1.56413 ( 6) link_BETA1-4 : bond 0.00424 ( 18) link_BETA1-4 : angle 1.91870 ( 54) link_BETA1-6 : bond 0.00900 ( 3) link_BETA1-6 : angle 2.43769 ( 9) link_NAG-ASN : bond 0.00624 ( 33) link_NAG-ASN : angle 3.77988 ( 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 189 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 192 MET cc_start: 0.8032 (mtm) cc_final: 0.7305 (mmt) REVERT: B 214 MET cc_start: 0.8403 (ptm) cc_final: 0.7687 (mtt) REVERT: B 247 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.5974 (tm130) REVERT: a 295 ASN cc_start: 0.7485 (m-40) cc_final: 0.7085 (t0) REVERT: a 307 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7785 (mm-30) REVERT: a 404 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7775 (mm-30) REVERT: a 409 ASN cc_start: 0.8603 (m110) cc_final: 0.8143 (m110) REVERT: b 282 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7785 (ttp80) REVERT: c 332 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6226 (ttt) outliers start: 20 outliers final: 17 residues processed: 178 average time/residue: 0.1086 time to fit residues: 26.6223 Evaluate side-chains 181 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain b residue 377 THR Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 402 ASP Chi-restraints excluded: chain c residue 265 THR Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 296 THR Chi-restraints excluded: chain c residue 332 MET Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 102 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 93 HIS ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS B 247 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.149069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.120872 restraints weight = 12224.685| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.33 r_work: 0.3175 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 10215 Z= 0.327 Angle : 0.852 15.904 13981 Z= 0.384 Chirality : 0.052 0.611 1748 Planarity : 0.004 0.071 1676 Dihedral : 8.322 59.386 2508 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.33 % Allowed : 9.42 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.26), residues: 971 helix: 0.22 (0.28), residues: 331 sheet: 0.09 (0.46), residues: 124 loop : -0.80 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 379 TYR 0.015 0.002 TYR C 217 PHE 0.017 0.002 PHE A 191 TRP 0.021 0.002 TRP C 227 HIS 0.007 0.002 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00780 (10135) covalent geometry : angle 0.76218 (13762) SS BOND : bond 0.00645 ( 21) SS BOND : angle 1.20740 ( 42) hydrogen bonds : bond 0.03905 ( 396) hydrogen bonds : angle 4.90573 ( 1062) link_ALPHA1-2 : bond 0.01269 ( 1) link_ALPHA1-2 : angle 3.09073 ( 3) link_ALPHA1-3 : bond 0.00699 ( 2) link_ALPHA1-3 : angle 2.04120 ( 6) link_ALPHA1-6 : bond 0.00208 ( 2) link_ALPHA1-6 : angle 1.82912 ( 6) link_BETA1-4 : bond 0.00537 ( 18) link_BETA1-4 : angle 2.13720 ( 54) link_BETA1-6 : bond 0.00575 ( 3) link_BETA1-6 : angle 2.83655 ( 9) link_NAG-ASN : bond 0.00800 ( 33) link_NAG-ASN : angle 4.14991 ( 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 182 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 192 MET cc_start: 0.8057 (mtm) cc_final: 0.7214 (mmt) REVERT: B 247 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.5858 (tm130) REVERT: a 295 ASN cc_start: 0.7458 (m-40) cc_final: 0.7006 (t0) REVERT: a 307 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7764 (mm-30) REVERT: a 404 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7765 (mm-30) REVERT: a 409 ASN cc_start: 0.8517 (m110) cc_final: 0.8067 (m110) REVERT: b 282 ARG cc_start: 0.8136 (ttp80) cc_final: 0.7903 (ttp80) REVERT: c 332 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6496 (ttt) outliers start: 21 outliers final: 18 residues processed: 170 average time/residue: 0.1017 time to fit residues: 24.1585 Evaluate side-chains 180 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain b residue 332 MET Chi-restraints excluded: chain b residue 377 THR Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain c residue 265 THR Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 296 THR Chi-restraints excluded: chain c residue 304 LYS Chi-restraints excluded: chain c residue 332 MET Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 40 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS c 354 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.162695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.138137 restraints weight = 11647.432| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.03 r_work: 0.3266 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10215 Z= 0.131 Angle : 0.679 14.041 13981 Z= 0.304 Chirality : 0.046 0.572 1748 Planarity : 0.003 0.040 1676 Dihedral : 7.809 59.796 2508 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.00 % Allowed : 9.98 % Favored : 88.03 % 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: -0.28 (0.26), residues: 971 helix: 0.55 (0.29), residues: 331 sheet: 0.09 (0.47), residues: 122 loop : -0.69 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 248 TYR 0.017 0.001 TYR B 150 PHE 0.012 0.001 PHE A 191 TRP 0.016 0.001 TRP C 227 HIS 0.004 0.001 HIS b 374 Details of bonding type rmsd covalent geometry : bond 0.00294 (10135) covalent geometry : angle 0.58414 (13762) SS BOND : bond 0.00297 ( 21) SS BOND : angle 0.84961 ( 42) hydrogen bonds : bond 0.03032 ( 396) hydrogen bonds : angle 4.55696 ( 1062) link_ALPHA1-2 : bond 0.01336 ( 1) link_ALPHA1-2 : angle 2.69778 ( 3) link_ALPHA1-3 : bond 0.00955 ( 2) link_ALPHA1-3 : angle 1.71596 ( 6) link_ALPHA1-6 : bond 0.00423 ( 2) link_ALPHA1-6 : angle 1.56211 ( 6) link_BETA1-4 : bond 0.00424 ( 18) link_BETA1-4 : angle 1.90071 ( 54) link_BETA1-6 : bond 0.00873 ( 3) link_BETA1-6 : angle 2.47042 ( 9) link_NAG-ASN : bond 0.00598 ( 33) link_NAG-ASN : angle 3.77797 ( 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 180 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.8269 (mmt) cc_final: 0.8003 (mmt) REVERT: C 192 MET cc_start: 0.8071 (mtm) cc_final: 0.7370 (mmt) REVERT: B 214 MET cc_start: 0.8423 (ptm) cc_final: 0.7682 (mtt) REVERT: B 247 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.6002 (tm-30) REVERT: a 295 ASN cc_start: 0.7470 (m-40) cc_final: 0.7079 (t0) REVERT: a 307 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7819 (mm-30) REVERT: a 404 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7806 (mm-30) REVERT: a 409 ASN cc_start: 0.8597 (m110) cc_final: 0.8137 (m110) REVERT: b 282 ARG cc_start: 0.8142 (ttp80) cc_final: 0.7919 (ttp80) REVERT: b 389 SER cc_start: 0.8818 (t) cc_final: 0.8557 (m) outliers start: 18 outliers final: 16 residues processed: 169 average time/residue: 0.1114 time to fit residues: 26.1173 Evaluate side-chains 178 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain a residue 265 THR Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain b residue 332 MET Chi-restraints excluded: chain b residue 377 THR Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 296 THR Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 63 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS c 354 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.161735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.136764 restraints weight = 11866.604| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.07 r_work: 0.3250 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10215 Z= 0.172 Angle : 0.697 14.292 13981 Z= 0.312 Chirality : 0.046 0.567 1748 Planarity : 0.003 0.042 1676 Dihedral : 7.650 59.697 2508 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.00 % Allowed : 10.31 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.26), residues: 971 helix: 0.58 (0.29), residues: 331 sheet: 0.14 (0.48), residues: 122 loop : -0.71 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 379 TYR 0.016 0.001 TYR B 150 PHE 0.014 0.001 PHE A 191 TRP 0.020 0.001 TRP C 227 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00402 (10135) covalent geometry : angle 0.60307 (13762) SS BOND : bond 0.00385 ( 21) SS BOND : angle 0.88130 ( 42) hydrogen bonds : bond 0.03183 ( 396) hydrogen bonds : angle 4.54235 ( 1062) link_ALPHA1-2 : bond 0.01301 ( 1) link_ALPHA1-2 : angle 2.80083 ( 3) link_ALPHA1-3 : bond 0.00897 ( 2) link_ALPHA1-3 : angle 1.86036 ( 6) link_ALPHA1-6 : bond 0.00336 ( 2) link_ALPHA1-6 : angle 1.62400 ( 6) link_BETA1-4 : bond 0.00387 ( 18) link_BETA1-4 : angle 1.88896 ( 54) link_BETA1-6 : bond 0.00794 ( 3) link_BETA1-6 : angle 2.54389 ( 9) link_NAG-ASN : bond 0.00612 ( 33) link_NAG-ASN : angle 3.80554 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2847.31 seconds wall clock time: 49 minutes 37.02 seconds (2977.02 seconds total)