Starting phenix.real_space_refine on Wed Apr 30 23:37:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ck8_45644/04_2025/9ck8_45644.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ck8_45644/04_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_45644/04_2025/9ck8_45644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ck8_45644/04_2025/9ck8_45644.map" model { file = "/net/cci-nas-00/data/ceres_data/9ck8_45644/04_2025/9ck8_45644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ck8_45644/04_2025/9ck8_45644.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 8.50, per 1000 atoms: 0.85 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: 3.00 Conformation dependent library (CDL) restraints added in 934.6 milliseconds 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: 1.06 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: 2.83 Time building geometry restraints manager: 3.45 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 259 or resid 301 throu \ gh 302)) selection = chain 'B' selection = (chain 'C' and (resid 60 through 202 or resid 207 through 259 or resid 301 throu \ gh 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 413 or resid 701 thro \ ugh 702)) selection = (chain 'b' and (resid 260 through 413 or resid 701 through 702)) selection = (chain 'c' and (resid 260 through 267 or resid 278 through 413 or resid 701 thro \ ugh 702)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 7.060 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.320 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.150 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (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 TRP 0.011 0.001 TRP A 227 HIS 0.010 0.001 HIS B 92 PHE 0.014 0.002 PHE a 399 TYR 0.023 0.002 TYR C 253 ARG 0.008 0.001 ARG C 193 Details of bonding type rmsd link_NAG-ASN : bond 0.02638 ( 33) link_NAG-ASN : angle 5.45196 ( 99) 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_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) hydrogen bonds : bond 0.15810 ( 396) hydrogen bonds : angle 6.36840 ( 1062) link_BETA1-6 : bond 0.00426 ( 3) link_BETA1-6 : angle 2.85187 ( 9) SS BOND : bond 0.00415 ( 21) SS BOND : angle 1.05194 ( 42) covalent geometry : bond 0.00544 (10135) covalent geometry : angle 0.88683 (13762) *********************** 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 : 1.038 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: 0.2523 time to fit residues: 64.1893 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 : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 91 optimal weight: 0.0870 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN 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 409 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.178643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.151669 restraints weight = 11636.474| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.27 r_work: 0.3627 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1110 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= 0.138 Angle : 0.718 14.020 13981 Z= 0.319 Chirality : 0.049 0.563 1748 Planarity : 0.003 0.036 1676 Dihedral : 8.871 77.246 2508 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.11 % Allowed : 4.32 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.27), residues: 971 helix: 0.48 (0.29), residues: 339 sheet: -0.49 (0.46), residues: 120 loop : -0.41 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 227 HIS 0.004 0.001 HIS A 115 PHE 0.017 0.001 PHE C 157 TYR 0.009 0.001 TYR B 253 ARG 0.004 0.000 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00809 ( 33) link_NAG-ASN : angle 4.19357 ( 99) link_ALPHA1-6 : bond 0.00670 ( 2) link_ALPHA1-6 : angle 1.55197 ( 6) link_BETA1-4 : bond 0.00481 ( 18) link_BETA1-4 : angle 2.04076 ( 54) link_ALPHA1-2 : bond 0.01524 ( 1) link_ALPHA1-2 : angle 2.67695 ( 3) link_ALPHA1-3 : bond 0.00767 ( 2) link_ALPHA1-3 : angle 1.73436 ( 6) hydrogen bonds : bond 0.03833 ( 396) hydrogen bonds : angle 4.91015 ( 1062) link_BETA1-6 : bond 0.00609 ( 3) link_BETA1-6 : angle 2.11554 ( 9) SS BOND : bond 0.00337 ( 21) SS BOND : angle 0.77700 ( 42) covalent geometry : bond 0.00301 (10135) covalent geometry : angle 0.61035 (13762) *********************** 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 182 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 1.030 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 121 SER cc_start: 0.8838 (p) cc_final: 0.8548 (t) REVERT: C 192 MET cc_start: 0.8220 (mtm) cc_final: 0.7718 (mmt) REVERT: B 214 MET cc_start: 0.8217 (ptm) cc_final: 0.7865 (mtt) REVERT: B 247 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.6652 (tm130) REVERT: a 307 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7883 (mm-30) REVERT: a 404 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7812 (mm-30) REVERT: b 409 ASN cc_start: 0.7728 (m110) cc_final: 0.7506 (m110) outliers start: 10 outliers final: 7 residues processed: 175 average time/residue: 0.2920 time to fit residues: 70.3885 Evaluate side-chains 171 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 163 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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 252 ILE Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain b residue 320 LYS 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 72 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 158 ASN B 247 GLN a 374 HIS b 346 ASN c 353 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.180253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.153362 restraints weight = 11662.095| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.22 r_work: 0.3643 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10215 Z= 0.167 Angle : 0.696 13.892 13981 Z= 0.312 Chirality : 0.047 0.554 1748 Planarity : 0.003 0.045 1676 Dihedral : 8.391 68.632 2508 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.88 % Allowed : 5.10 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.27), residues: 971 helix: 0.44 (0.29), residues: 339 sheet: -0.48 (0.46), residues: 128 loop : -0.35 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 227 HIS 0.005 0.001 HIS A 124 PHE 0.012 0.001 PHE C 157 TYR 0.014 0.001 TYR C 94 ARG 0.003 0.000 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00709 ( 33) link_NAG-ASN : angle 4.03922 ( 99) link_ALPHA1-6 : bond 0.00465 ( 2) link_ALPHA1-6 : angle 1.66418 ( 6) link_BETA1-4 : bond 0.00393 ( 18) link_BETA1-4 : angle 1.99260 ( 54) link_ALPHA1-2 : bond 0.01303 ( 1) link_ALPHA1-2 : angle 2.40115 ( 3) link_ALPHA1-3 : bond 0.00814 ( 2) link_ALPHA1-3 : angle 1.75591 ( 6) hydrogen bonds : bond 0.03337 ( 396) hydrogen bonds : angle 4.71395 ( 1062) link_BETA1-6 : bond 0.00502 ( 3) link_BETA1-6 : angle 2.26902 ( 9) SS BOND : bond 0.00338 ( 21) SS BOND : angle 0.83393 ( 42) covalent geometry : bond 0.00387 (10135) covalent geometry : angle 0.59108 (13762) *********************** 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 189 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 1.362 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 94 TYR cc_start: 0.8713 (m-80) cc_final: 0.8496 (m-80) REVERT: C 192 MET cc_start: 0.8249 (mtm) cc_final: 0.7696 (mmt) REVERT: B 214 MET cc_start: 0.8327 (ptm) cc_final: 0.7865 (mtt) REVERT: B 247 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.6419 (tm130) REVERT: a 307 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7969 (mm-30) REVERT: a 404 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7825 (mm-30) REVERT: a 409 ASN cc_start: 0.8673 (m-40) cc_final: 0.8306 (m110) REVERT: b 290 LEU cc_start: 0.8203 (tp) cc_final: 0.7955 (tp) outliers start: 17 outliers final: 15 residues processed: 175 average time/residue: 0.2942 time to fit residues: 72.5615 Evaluate side-chains 182 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 1.589 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 76 optimal weight: 0.2980 chunk 68 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 405 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.182235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.156213 restraints weight = 11518.749| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.14 r_work: 0.3670 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10215 Z= 0.110 Angle : 0.631 13.033 13981 Z= 0.281 Chirality : 0.044 0.517 1748 Planarity : 0.003 0.037 1676 Dihedral : 7.794 63.837 2508 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.00 % Allowed : 6.32 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.27), residues: 971 helix: 0.64 (0.29), residues: 339 sheet: -0.13 (0.47), residues: 122 loop : -0.36 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 227 HIS 0.003 0.001 HIS A 115 PHE 0.010 0.001 PHE A 191 TYR 0.015 0.001 TYR B 150 ARG 0.003 0.000 ARG c 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00695 ( 33) link_NAG-ASN : angle 3.79987 ( 99) link_ALPHA1-6 : bond 0.00516 ( 2) link_ALPHA1-6 : angle 1.70772 ( 6) link_BETA1-4 : bond 0.00424 ( 18) link_BETA1-4 : angle 1.90924 ( 54) link_ALPHA1-2 : bond 0.01329 ( 1) link_ALPHA1-2 : angle 2.34691 ( 3) link_ALPHA1-3 : bond 0.00988 ( 2) link_ALPHA1-3 : angle 1.73406 ( 6) hydrogen bonds : bond 0.02885 ( 396) hydrogen bonds : angle 4.49468 ( 1062) link_BETA1-6 : bond 0.00640 ( 3) link_BETA1-6 : angle 2.12236 ( 9) SS BOND : bond 0.00252 ( 21) SS BOND : angle 0.70120 ( 42) covalent geometry : bond 0.00236 (10135) covalent geometry : angle 0.52731 (13762) *********************** 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 188 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.952 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 100 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7964 (mm-30) REVERT: C 192 MET cc_start: 0.8217 (mtm) cc_final: 0.7654 (mmt) REVERT: B 214 MET cc_start: 0.8347 (ptm) cc_final: 0.7865 (mtt) REVERT: a 307 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7927 (mm-30) REVERT: a 404 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7769 (mm-30) REVERT: a 409 ASN cc_start: 0.8663 (m-40) cc_final: 0.8269 (m110) outliers start: 18 outliers final: 13 residues processed: 176 average time/residue: 0.2244 time to fit residues: 54.9789 Evaluate side-chains 180 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 252 ILE Chi-restraints excluded: chain B residue 234 SER 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 388 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 90 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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** B 247 GLN b 374 HIS c 354 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.173550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146639 restraints weight = 11578.215| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.16 r_work: 0.3563 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 10215 Z= 0.294 Angle : 0.842 15.565 13981 Z= 0.377 Chirality : 0.052 0.645 1748 Planarity : 0.004 0.071 1676 Dihedral : 8.439 58.694 2508 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.33 % Allowed : 6.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.26), residues: 971 helix: 0.29 (0.28), residues: 331 sheet: 0.01 (0.47), residues: 121 loop : -0.67 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 227 HIS 0.009 0.002 HIS A 124 PHE 0.017 0.002 PHE A 191 TYR 0.017 0.002 TYR C 62 ARG 0.005 0.001 ARG C 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00763 ( 33) link_NAG-ASN : angle 4.25293 ( 99) link_ALPHA1-6 : bond 0.00113 ( 2) link_ALPHA1-6 : angle 1.78755 ( 6) link_BETA1-4 : bond 0.00476 ( 18) link_BETA1-4 : angle 2.13923 ( 54) link_ALPHA1-2 : bond 0.01086 ( 1) link_ALPHA1-2 : angle 2.82796 ( 3) link_ALPHA1-3 : bond 0.00739 ( 2) link_ALPHA1-3 : angle 2.21800 ( 6) hydrogen bonds : bond 0.03869 ( 396) hydrogen bonds : angle 4.96457 ( 1062) link_BETA1-6 : bond 0.00461 ( 3) link_BETA1-6 : angle 2.74087 ( 9) SS BOND : bond 0.00777 ( 21) SS BOND : angle 1.13480 ( 42) covalent geometry : bond 0.00694 (10135) covalent geometry : angle 0.74717 (13762) *********************** 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 187 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 1.073 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: 0.8287 (mtm) cc_final: 0.7702 (mmt) REVERT: B 214 MET cc_start: 0.8384 (ptm) cc_final: 0.7839 (mtt) REVERT: B 247 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.6528 (tm130) REVERT: a 307 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8063 (mm-30) REVERT: a 404 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7861 (mm-30) REVERT: a 409 ASN cc_start: 0.8682 (m-40) cc_final: 0.8258 (m110) outliers start: 21 outliers final: 16 residues processed: 172 average time/residue: 0.2379 time to fit residues: 56.2138 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 : 1.116 ------------------------------------------------------------------------------- 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 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 388 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 b 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 = 0.4076 r_free = 0.4076 target = 0.178034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.151157 restraints weight = 11625.810| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.19 r_work: 0.3618 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10215 Z= 0.132 Angle : 0.674 13.688 13981 Z= 0.301 Chirality : 0.046 0.548 1748 Planarity : 0.003 0.040 1676 Dihedral : 7.830 58.938 2508 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.11 % Allowed : 6.98 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.26), residues: 971 helix: 0.60 (0.29), residues: 331 sheet: -0.06 (0.47), residues: 122 loop : -0.58 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 227 HIS 0.003 0.001 HIS A 115 PHE 0.014 0.001 PHE A 233 TYR 0.013 0.001 TYR B 150 ARG 0.006 0.000 ARG B 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00683 ( 33) link_NAG-ASN : angle 3.84909 ( 99) link_ALPHA1-6 : bond 0.00437 ( 2) link_ALPHA1-6 : angle 1.62976 ( 6) link_BETA1-4 : bond 0.00435 ( 18) link_BETA1-4 : angle 1.94132 ( 54) link_ALPHA1-2 : bond 0.01246 ( 1) link_ALPHA1-2 : angle 2.54416 ( 3) link_ALPHA1-3 : bond 0.01054 ( 2) link_ALPHA1-3 : angle 1.83557 ( 6) hydrogen bonds : bond 0.03010 ( 396) hydrogen bonds : angle 4.60845 ( 1062) link_BETA1-6 : bond 0.00777 ( 3) link_BETA1-6 : angle 2.37475 ( 9) SS BOND : bond 0.00411 ( 21) SS BOND : angle 0.77418 ( 42) covalent geometry : bond 0.00296 (10135) covalent geometry : angle 0.57462 (13762) *********************** 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 181 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.984 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: 0.8235 (mtm) cc_final: 0.7691 (mmt) REVERT: B 214 MET cc_start: 0.8367 (ptm) cc_final: 0.7842 (mtt) REVERT: B 247 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.6387 (tm130) REVERT: a 307 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8052 (mm-30) REVERT: a 404 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7835 (mm-30) REVERT: a 409 ASN cc_start: 0.8678 (m-40) cc_final: 0.8313 (m110) outliers start: 19 outliers final: 16 residues processed: 169 average time/residue: 0.2504 time to fit residues: 57.8723 Evaluate side-chains 175 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 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 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 304 LYS 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 9 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 106 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 354 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.176348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.149486 restraints weight = 11659.652| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.19 r_work: 0.3600 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10215 Z= 0.178 Angle : 0.704 14.048 13981 Z= 0.313 Chirality : 0.046 0.549 1748 Planarity : 0.003 0.046 1676 Dihedral : 7.790 59.638 2508 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.88 % Allowed : 7.10 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.26), residues: 971 helix: 0.56 (0.29), residues: 331 sheet: -0.01 (0.47), residues: 122 loop : -0.63 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 227 HIS 0.004 0.001 HIS A 124 PHE 0.014 0.001 PHE A 191 TYR 0.014 0.001 TYR B 150 ARG 0.006 0.001 ARG b 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00656 ( 33) link_NAG-ASN : angle 4.05191 ( 99) link_ALPHA1-6 : bond 0.00310 ( 2) link_ALPHA1-6 : angle 1.63339 ( 6) link_BETA1-4 : bond 0.00389 ( 18) link_BETA1-4 : angle 1.97482 ( 54) link_ALPHA1-2 : bond 0.01171 ( 1) link_ALPHA1-2 : angle 2.68672 ( 3) link_ALPHA1-3 : bond 0.00886 ( 2) link_ALPHA1-3 : angle 1.89004 ( 6) hydrogen bonds : bond 0.03193 ( 396) hydrogen bonds : angle 4.60411 ( 1062) link_BETA1-6 : bond 0.00686 ( 3) link_BETA1-6 : angle 2.48567 ( 9) SS BOND : bond 0.00373 ( 21) SS BOND : angle 0.82922 ( 42) covalent geometry : bond 0.00416 (10135) covalent geometry : angle 0.60005 (13762) *********************** 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 187 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 1.608 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: 0.8218 (mtm) cc_final: 0.7666 (mmt) REVERT: B 214 MET cc_start: 0.8371 (ptm) cc_final: 0.7822 (mtt) REVERT: B 247 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.6417 (tm130) REVERT: a 307 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8046 (mm-30) REVERT: a 404 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7826 (mm-30) REVERT: a 409 ASN cc_start: 0.8725 (m-40) cc_final: 0.8346 (m110) REVERT: c 332 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6440 (ttt) outliers start: 26 outliers final: 20 residues processed: 170 average time/residue: 0.3225 time to fit residues: 77.0210 Evaluate side-chains 181 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 410 MET 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 304 LYS 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 116 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 354 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.150751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.122876 restraints weight = 12127.655| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.28 r_work: 0.3200 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10215 Z= 0.263 Angle : 0.794 15.108 13981 Z= 0.354 Chirality : 0.050 0.583 1748 Planarity : 0.004 0.057 1676 Dihedral : 8.110 57.090 2508 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.99 % Allowed : 7.43 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.26), residues: 971 helix: 0.36 (0.28), residues: 331 sheet: 0.18 (0.47), residues: 118 loop : -0.76 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 227 HIS 0.007 0.001 HIS A 124 PHE 0.016 0.002 PHE A 191 TYR 0.015 0.002 TYR B 150 ARG 0.006 0.001 ARG B 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00699 ( 33) link_NAG-ASN : angle 4.35340 ( 99) link_ALPHA1-6 : bond 0.00203 ( 2) link_ALPHA1-6 : angle 1.74240 ( 6) link_BETA1-4 : bond 0.00455 ( 18) link_BETA1-4 : angle 2.07022 ( 54) link_ALPHA1-2 : bond 0.01202 ( 1) link_ALPHA1-2 : angle 2.91269 ( 3) link_ALPHA1-3 : bond 0.00746 ( 2) link_ALPHA1-3 : angle 1.97651 ( 6) hydrogen bonds : bond 0.03583 ( 396) hydrogen bonds : angle 4.78121 ( 1062) link_BETA1-6 : bond 0.00592 ( 3) link_BETA1-6 : angle 2.67124 ( 9) SS BOND : bond 0.00518 ( 21) SS BOND : angle 0.98779 ( 42) covalent geometry : bond 0.00626 (10135) covalent geometry : angle 0.68862 (13762) *********************** 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 183 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.025 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: 0.8028 (mtm) cc_final: 0.7197 (mmt) REVERT: B 214 MET cc_start: 0.8474 (ptm) cc_final: 0.7656 (mtt) REVERT: B 247 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.5968 (tm130) REVERT: a 307 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7760 (mm-30) REVERT: a 404 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7777 (mm-30) REVERT: b 282 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7781 (ttp80) REVERT: c 332 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6293 (ttt) outliers start: 27 outliers final: 21 residues processed: 168 average time/residue: 0.2571 time to fit residues: 59.0458 Evaluate side-chains 177 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 410 MET 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 0.5980 chunk 18 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 83 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 78 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 b 398 HIS c 354 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.164344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.139668 restraints weight = 11645.962| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.03 r_work: 0.3289 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10215 Z= 0.118 Angle : 0.699 16.249 13981 Z= 0.307 Chirality : 0.045 0.547 1748 Planarity : 0.003 0.039 1676 Dihedral : 7.683 57.436 2508 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.33 % Allowed : 7.76 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 971 helix: 0.69 (0.29), residues: 331 sheet: 0.11 (0.47), residues: 122 loop : -0.66 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 227 HIS 0.003 0.001 HIS A 115 PHE 0.011 0.001 PHE A 191 TYR 0.016 0.001 TYR c 393 ARG 0.005 0.001 ARG B 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00641 ( 33) link_NAG-ASN : angle 4.36531 ( 99) link_ALPHA1-6 : bond 0.00461 ( 2) link_ALPHA1-6 : angle 1.52797 ( 6) link_BETA1-4 : bond 0.00438 ( 18) link_BETA1-4 : angle 1.86977 ( 54) link_ALPHA1-2 : bond 0.01319 ( 1) link_ALPHA1-2 : angle 2.58558 ( 3) link_ALPHA1-3 : bond 0.00971 ( 2) link_ALPHA1-3 : angle 1.68221 ( 6) hydrogen bonds : bond 0.02929 ( 396) hydrogen bonds : angle 4.51419 ( 1062) link_BETA1-6 : bond 0.00893 ( 3) link_BETA1-6 : angle 2.40028 ( 9) SS BOND : bond 0.00273 ( 21) SS BOND : angle 0.93984 ( 42) covalent geometry : bond 0.00257 (10135) covalent geometry : angle 0.57872 (13762) *********************** 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 187 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 1.027 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 75 MET cc_start: 0.8229 (mmt) cc_final: 0.8025 (mmt) REVERT: C 192 MET cc_start: 0.8025 (mtm) cc_final: 0.7313 (mmt) REVERT: B 214 MET cc_start: 0.8392 (ptm) cc_final: 0.7686 (mtt) REVERT: B 234 SER cc_start: 0.9342 (OUTLIER) cc_final: 0.8844 (m) REVERT: B 247 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.6077 (tm130) REVERT: a 307 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7774 (mm-30) REVERT: a 404 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7750 (mm-30) REVERT: b 282 ARG cc_start: 0.8012 (ttp80) cc_final: 0.7790 (ttp80) REVERT: c 332 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6121 (ttt) outliers start: 21 outliers final: 15 residues processed: 174 average time/residue: 0.2451 time to fit residues: 58.2298 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 : 1.007 ------------------------------------------------------------------------------- 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 341 VAL Chi-restraints excluded: chain a residue 376 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 402 ASP Chi-restraints excluded: chain c residue 265 THR Chi-restraints excluded: chain c residue 290 LEU Chi-restraints excluded: chain c residue 304 LYS Chi-restraints excluded: chain c residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 53 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS B 69 GLN c 354 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.163637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.139007 restraints weight = 11688.921| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.01 r_work: 0.3283 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2597 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= 0.135 Angle : 0.680 13.922 13981 Z= 0.302 Chirality : 0.045 0.537 1748 Planarity : 0.003 0.038 1676 Dihedral : 7.516 57.127 2508 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.00 % Allowed : 8.31 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.26), residues: 971 helix: 0.73 (0.29), residues: 331 sheet: 0.20 (0.47), residues: 122 loop : -0.65 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 227 HIS 0.003 0.001 HIS A 115 PHE 0.012 0.001 PHE A 191 TYR 0.020 0.001 TYR B 150 ARG 0.006 0.000 ARG b 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00598 ( 33) link_NAG-ASN : angle 4.14141 ( 99) link_ALPHA1-6 : bond 0.00407 ( 2) link_ALPHA1-6 : angle 1.55493 ( 6) link_BETA1-4 : bond 0.00397 ( 18) link_BETA1-4 : angle 1.84630 ( 54) link_ALPHA1-2 : bond 0.01289 ( 1) link_ALPHA1-2 : angle 2.59712 ( 3) link_ALPHA1-3 : bond 0.00963 ( 2) link_ALPHA1-3 : angle 1.79790 ( 6) hydrogen bonds : bond 0.02976 ( 396) hydrogen bonds : angle 4.44471 ( 1062) link_BETA1-6 : bond 0.00825 ( 3) link_BETA1-6 : angle 2.44944 ( 9) SS BOND : bond 0.00306 ( 21) SS BOND : angle 0.84763 ( 42) covalent geometry : bond 0.00308 (10135) covalent geometry : angle 0.56853 (13762) ********************** 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 182 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 1.002 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 75 MET cc_start: 0.8288 (mmt) cc_final: 0.8009 (mmt) REVERT: C 192 MET cc_start: 0.8038 (mtm) cc_final: 0.7322 (mmt) REVERT: B 214 MET cc_start: 0.8392 (ptm) cc_final: 0.7703 (mtt) REVERT: B 234 SER cc_start: 0.9330 (OUTLIER) cc_final: 0.8837 (m) REVERT: B 247 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.5906 (tm-30) REVERT: a 295 ASN cc_start: 0.7553 (m-40) cc_final: 0.7151 (t0) REVERT: a 307 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7764 (mm-30) REVERT: a 404 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7731 (mm-30) REVERT: b 282 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7795 (ttp80) REVERT: c 332 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6237 (ttt) outliers start: 18 outliers final: 13 residues processed: 172 average time/residue: 0.2500 time to fit residues: 58.6320 Evaluate side-chains 179 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 341 VAL Chi-restraints excluded: chain a residue 376 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 402 ASP Chi-restraints excluded: chain c residue 265 THR Chi-restraints excluded: chain c residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 86 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 112 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.164034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.138815 restraints weight = 11748.353| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.09 r_work: 0.3279 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10215 Z= 0.137 Angle : 0.661 13.020 13981 Z= 0.295 Chirality : 0.044 0.525 1748 Planarity : 0.003 0.038 1676 Dihedral : 7.227 58.720 2508 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.88 % Allowed : 8.54 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.26), residues: 971 helix: 0.78 (0.29), residues: 331 sheet: 0.30 (0.47), residues: 122 loop : -0.64 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 227 HIS 0.003 0.001 HIS b 374 PHE 0.012 0.001 PHE A 191 TYR 0.019 0.001 TYR B 150 ARG 0.002 0.000 ARG c 356 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 33) link_NAG-ASN : angle 3.94592 ( 99) link_ALPHA1-6 : bond 0.00438 ( 2) link_ALPHA1-6 : angle 1.55403 ( 6) link_BETA1-4 : bond 0.00377 ( 18) link_BETA1-4 : angle 1.78998 ( 54) link_ALPHA1-2 : bond 0.01293 ( 1) link_ALPHA1-2 : angle 2.48028 ( 3) link_ALPHA1-3 : bond 0.00967 ( 2) link_ALPHA1-3 : angle 1.76146 ( 6) hydrogen bonds : bond 0.02923 ( 396) hydrogen bonds : angle 4.38491 ( 1062) link_BETA1-6 : bond 0.00788 ( 3) link_BETA1-6 : angle 2.44858 ( 9) SS BOND : bond 0.00313 ( 21) SS BOND : angle 0.82446 ( 42) covalent geometry : bond 0.00313 (10135) covalent geometry : angle 0.55681 (13762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6001.62 seconds wall clock time: 106 minutes 38.70 seconds (6398.70 seconds total)