Starting phenix.real_space_refine on Wed Mar 4 14:28:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dmh_27538/03_2026/8dmh_27538.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmh_27538/03_2026/8dmh_27538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dmh_27538/03_2026/8dmh_27538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmh_27538/03_2026/8dmh_27538.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dmh_27538/03_2026/8dmh_27538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmh_27538/03_2026/8dmh_27538.map" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 102 5.16 5 C 8988 2.51 5 N 2379 2.21 5 O 2790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14259 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1521 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 1 Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 822 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "F" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 938 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "a" Number of atoms: 1265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1265 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "B" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1521 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 1 Chain: "G" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 822 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 938 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "b" Number of atoms: 1265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1265 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "C" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1521 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 1 Chain: "I" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 822 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "J" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 938 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "c" Number of atoms: 1265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1265 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.36, per 1000 atoms: 0.24 Number of scatterers: 14259 At special positions: 0 Unit cell: (118.8, 128.4, 103.2, 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 102 16.00 O 2790 8.00 N 2379 7.00 C 8988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 123 " - pdb=" SG CYS A 160 " distance=2.04 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 366 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 98 " distance=2.03 Simple disulfide: pdb=" SG CYS a 285 " - pdb=" SG CYS a 298 " distance=2.04 Simple disulfide: pdb=" SG CYS a 307 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS a 370 " - pdb=" SG CYS a 391 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 123 " - pdb=" SG CYS B 160 " distance=2.04 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 366 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS b 285 " - pdb=" SG CYS b 298 " distance=2.04 Simple disulfide: pdb=" SG CYS b 307 " - pdb=" SG CYS b 316 " distance=2.03 Simple disulfide: pdb=" SG CYS b 370 " - pdb=" SG CYS b 391 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 123 " - pdb=" SG CYS C 160 " distance=2.03 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 366 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 89 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 98 " distance=2.03 Simple disulfide: pdb=" SG CYS c 285 " - pdb=" SG CYS c 298 " distance=2.04 Simple disulfide: pdb=" SG CYS c 307 " - pdb=" SG CYS c 316 " distance=2.03 Simple disulfide: pdb=" SG CYS c 370 " - pdb=" SG CYS c 391 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A 301 " - " ASN A 124 " " NAG B 301 " - " ASN B 124 " " NAG C 301 " - " ASN C 124 " " NAG D 1 " - " ASN A 85 " " NAG K 1 " - " ASN A 95 " " NAG L 1 " - " ASN A 114 " " NAG M 1 " - " ASN A 171 " " NAG N 1 " - " ASN A 232 " " NAG O 1 " - " ASN a 401 " " NAG P 1 " - " ASN B 85 " " NAG Q 1 " - " ASN B 95 " " NAG R 1 " - " ASN B 114 " " NAG S 1 " - " ASN B 171 " " NAG T 1 " - " ASN B 232 " " NAG U 1 " - " ASN b 401 " " NAG V 1 " - " ASN C 85 " " NAG W 1 " - " ASN C 95 " " NAG X 1 " - " ASN C 114 " " NAG Y 1 " - " ASN C 171 " " NAG Z 1 " - " ASN C 232 " " NAG a 701 " - " ASN a 371 " " NAG b 701 " - " ASN b 371 " " NAG c 701 " - " ASN c 371 " " NAG d 1 " - " ASN c 401 " Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 491.7 milliseconds 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3198 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 26 sheets defined 25.9% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.551A pdb=" N ASN A 85 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU A 86 " --> pdb=" O HIS A 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 86' Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.692A pdb=" N ILE A 141 " --> pdb=" O THR A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 removed outlier: 3.573A pdb=" N MET A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.674A pdb=" N TRP A 210 " --> pdb=" O CYS A 207 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR A 211 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A 212 " --> pdb=" O GLY A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 212' Processing helix chain 'A' and resid 244 through 254 removed outlier: 3.804A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'F' and resid 89 through 93 removed outlier: 3.509A pdb=" N THR F 93 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 300 through 308 removed outlier: 3.523A pdb=" N VAL a 304 " --> pdb=" O GLY a 300 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS a 306 " --> pdb=" O THR a 302 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS a 307 " --> pdb=" O ALA a 303 " (cutoff:3.500A) Processing helix chain 'a' and resid 313 through 332 removed outlier: 3.976A pdb=" N ASP a 317 " --> pdb=" O GLU a 313 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET a 318 " --> pdb=" O GLU a 314 " (cutoff:3.500A) Processing helix chain 'a' and resid 335 through 346 removed outlier: 3.755A pdb=" N HIS a 341 " --> pdb=" O GLU a 337 " (cutoff:3.500A) Processing helix chain 'a' and resid 347 through 351 Processing helix chain 'a' and resid 352 through 365 Processing helix chain 'a' and resid 401 through 404 Processing helix chain 'a' and resid 405 through 427 removed outlier: 3.667A pdb=" N LYS a 423 " --> pdb=" O GLU a 419 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE a 426 " --> pdb=" O ARG a 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 130 removed outlier: 4.069A pdb=" N ASN B 130 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 147 Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 244 through 252 removed outlier: 3.509A pdb=" N ARG B 249 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 250 " --> pdb=" O GLY B 246 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'H' and resid 89 through 93 removed outlier: 3.611A pdb=" N THR H 93 " --> pdb=" O ALA H 90 " (cutoff:3.500A) Processing helix chain 'b' and resid 287 through 291 removed outlier: 3.530A pdb=" N ILE b 291 " --> pdb=" O LYS b 288 " (cutoff:3.500A) Processing helix chain 'b' and resid 300 through 308 removed outlier: 3.928A pdb=" N LYS b 306 " --> pdb=" O THR b 302 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS b 307 " --> pdb=" O ALA b 303 " (cutoff:3.500A) Processing helix chain 'b' and resid 313 through 332 removed outlier: 3.951A pdb=" N ASP b 317 " --> pdb=" O GLU b 313 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET b 318 " --> pdb=" O GLU b 314 " (cutoff:3.500A) Processing helix chain 'b' and resid 335 through 346 Processing helix chain 'b' and resid 347 through 351 Processing helix chain 'b' and resid 352 through 365 removed outlier: 3.504A pdb=" N HIS b 360 " --> pdb=" O LEU b 356 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU b 361 " --> pdb=" O MET b 357 " (cutoff:3.500A) Processing helix chain 'b' and resid 401 through 404 Processing helix chain 'b' and resid 405 through 427 removed outlier: 3.500A pdb=" N GLU b 412 " --> pdb=" O GLN b 408 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS b 423 " --> pdb=" O GLU b 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 147 removed outlier: 3.565A pdb=" N ILE C 141 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 207 through 211 removed outlier: 3.917A pdb=" N TRP C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR C 211 " --> pdb=" O TRP C 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 207 through 211' Processing helix chain 'C' and resid 244 through 253 removed outlier: 3.673A pdb=" N LEU C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER C 253 " --> pdb=" O ARG C 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 32 No H-bonds generated for 'chain 'I' and resid 30 through 32' Processing helix chain 'I' and resid 51 through 53 No H-bonds generated for 'chain 'I' and resid 51 through 53' Processing helix chain 'I' and resid 80 through 84 removed outlier: 4.170A pdb=" N PHE I 84 " --> pdb=" O PRO I 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 33 removed outlier: 3.540A pdb=" N ARG J 32 " --> pdb=" O THR J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 93 removed outlier: 3.552A pdb=" N THR J 93 " --> pdb=" O ALA J 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 287 through 291 Processing helix chain 'c' and resid 300 through 310 removed outlier: 3.592A pdb=" N VAL c 304 " --> pdb=" O GLY c 300 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS c 306 " --> pdb=" O THR c 302 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N CYS c 307 " --> pdb=" O ALA c 303 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN c 308 " --> pdb=" O VAL c 304 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL c 309 " --> pdb=" O ALA c 305 " (cutoff:3.500A) Processing helix chain 'c' and resid 313 through 332 removed outlier: 3.888A pdb=" N ASP c 317 " --> pdb=" O GLU c 313 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET c 318 " --> pdb=" O GLU c 314 " (cutoff:3.500A) Processing helix chain 'c' and resid 335 through 346 Processing helix chain 'c' and resid 347 through 351 Processing helix chain 'c' and resid 352 through 365 Processing helix chain 'c' and resid 401 through 404 Processing helix chain 'c' and resid 405 through 427 removed outlier: 3.510A pdb=" N THR c 418 " --> pdb=" O ASP c 414 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS c 423 " --> pdb=" O GLU c 419 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE c 426 " --> pdb=" O ARG c 422 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 93 removed outlier: 3.659A pdb=" N ILE A 101 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.647A pdb=" N LEU E 74 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP E 71 " --> pdb=" O SER E 68 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER E 66 " --> pdb=" O THR E 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.234A pdb=" N LEU E 11 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.234A pdb=" N LEU E 11 " --> pdb=" O GLU E 107 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 11 through 13 removed outlier: 6.993A pdb=" N MET F 35 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER F 51 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP F 37 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 20 through 23 removed outlier: 3.576A pdb=" N SER F 80 " --> pdb=" O ASP F 75 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER F 73 " --> pdb=" O TYR F 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 394 through 395 Processing sheet with id=AA9, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 93 removed outlier: 3.520A pdb=" N ILE B 101 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 4 through 6 removed outlier: 3.593A pdb=" N ALA G 19 " --> pdb=" O ILE G 76 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR G 73 " --> pdb=" O SER G 66 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER G 66 " --> pdb=" O THR G 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.182A pdb=" N LEU G 11 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TYR G 50 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.182A pdb=" N LEU G 11 " --> pdb=" O GLU G 107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.547A pdb=" N ALA H 94 " --> pdb=" O VAL H 120 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN H 36 " --> pdb=" O ALA H 99 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N MET H 35 " --> pdb=" O SER H 51 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N SER H 51 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP H 37 " --> pdb=" O VAL H 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 21 through 23 removed outlier: 3.579A pdb=" N SER H 80 " --> pdb=" O ASP H 75 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER H 73 " --> pdb=" O TYR H 82 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 285 through 286 removed outlier: 4.065A pdb=" N LYS b 297 " --> pdb=" O LEU b 286 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 394 through 395 Processing sheet with id=AB9, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AC1, first strand: chain 'C' and resid 90 through 93 Processing sheet with id=AC2, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.566A pdb=" N ALA I 19 " --> pdb=" O ILE I 76 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR I 75 " --> pdb=" O SER I 64 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.131A pdb=" N LEU I 11 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TYR I 50 " --> pdb=" O VAL I 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N LYS I 40 " --> pdb=" O ALA I 44 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ALA I 44 " --> pdb=" O LYS I 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.131A pdb=" N LEU I 11 " --> pdb=" O GLU I 107 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 7 through 8 removed outlier: 3.905A pdb=" N SER J 22 " --> pdb=" O SER J 8 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER J 73 " --> pdb=" O TYR J 82 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.520A pdb=" N GLY J 11 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N MET J 35 " --> pdb=" O SER J 51 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER J 51 " --> pdb=" O MET J 35 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP J 37 " --> pdb=" O VAL J 49 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'c' and resid 285 through 286 removed outlier: 3.551A pdb=" N LEU c 286 " --> pdb=" O LYS c 297 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS c 297 " --> pdb=" O LEU c 286 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'c' and resid 394 through 395 502 hydrogen bonds defined for protein. 1308 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: 2.42 Time building geometry restraints manager: 1.55 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: 4383 1.34 - 1.46: 4032 1.46 - 1.59: 6015 1.59 - 1.71: 0 1.71 - 1.83: 150 Bond restraints: 14580 Sorted by residual: bond pdb=" CB CYS C 92 " pdb=" SG CYS C 92 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CA TRP b 289 " pdb=" C TRP b 289 " ideal model delta sigma weight residual 1.523 1.502 0.021 1.80e-02 3.09e+03 1.35e+00 bond pdb=" CA VAL c 367 " pdb=" CB VAL c 367 " ideal model delta sigma weight residual 1.547 1.536 0.011 1.10e-02 8.26e+03 9.38e-01 bond pdb=" CG LEU c 393 " pdb=" CD1 LEU c 393 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.70e-01 bond pdb=" C1 NAG N 1 " pdb=" C2 NAG N 1 " ideal model delta sigma weight residual 1.532 1.550 -0.018 2.00e-02 2.50e+03 8.27e-01 ... (remaining 14575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 19323 1.82 - 3.63: 349 3.63 - 5.45: 37 5.45 - 7.27: 11 7.27 - 9.09: 2 Bond angle restraints: 19722 Sorted by residual: angle pdb=" CA TRP b 289 " pdb=" C TRP b 289 " pdb=" N MET b 290 " ideal model delta sigma weight residual 118.27 113.39 4.88 1.59e+00 3.96e-01 9.43e+00 angle pdb=" CB MET b 290 " pdb=" CG MET b 290 " pdb=" SD MET b 290 " ideal model delta sigma weight residual 112.70 103.61 9.09 3.00e+00 1.11e-01 9.17e+00 angle pdb=" CA MET b 290 " pdb=" CB MET b 290 " pdb=" CG MET b 290 " ideal model delta sigma weight residual 114.10 119.81 -5.71 2.00e+00 2.50e-01 8.15e+00 angle pdb=" N ASN A 232 " pdb=" CA ASN A 232 " pdb=" CB ASN A 232 " ideal model delta sigma weight residual 110.45 114.70 -4.25 1.52e+00 4.33e-01 7.83e+00 angle pdb=" CA CYS b 298 " pdb=" CB CYS b 298 " pdb=" SG CYS b 298 " ideal model delta sigma weight residual 114.40 120.47 -6.07 2.30e+00 1.89e-01 6.96e+00 ... (remaining 19717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.04: 8391 22.04 - 44.07: 626 44.07 - 66.11: 107 66.11 - 88.14: 43 88.14 - 110.18: 22 Dihedral angle restraints: 9189 sinusoidal: 4194 harmonic: 4995 Sorted by residual: dihedral pdb=" CB CYS A 92 " pdb=" SG CYS A 92 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual -86.00 -175.77 89.77 1 1.00e+01 1.00e-02 9.56e+01 dihedral pdb=" CB CYS B 92 " pdb=" SG CYS B 92 " pdb=" SG CYS B 239 " pdb=" CB CYS B 239 " ideal model delta sinusoidal sigma weight residual 93.00 43.02 49.98 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CA CYS c 298 " pdb=" C CYS c 298 " pdb=" N PHE c 299 " pdb=" CA PHE c 299 " ideal model delta harmonic sigma weight residual -180.00 -153.16 -26.84 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 9186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2146 0.088 - 0.175: 125 0.175 - 0.263: 3 0.263 - 0.351: 0 0.351 - 0.438: 3 Chirality restraints: 2277 Sorted by residual: chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN C 95 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 114 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN A 171 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 2274 not shown) Planarity restraints: 2445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN a 371 " 0.030 2.00e-02 2.50e+03 2.78e-02 9.68e+00 pdb=" CG ASN a 371 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN a 371 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN a 371 " -0.018 2.00e-02 2.50e+03 pdb=" C1 NAG a 701 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN c 401 " 0.025 2.00e-02 2.50e+03 2.40e-02 7.20e+00 pdb=" CG ASN c 401 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN c 401 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN c 401 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG d 1 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 114 " 0.025 2.00e-02 2.50e+03 2.35e-02 6.91e+00 pdb=" CG ASN B 114 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN B 114 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 114 " -0.026 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " 0.025 2.00e-02 2.50e+03 ... (remaining 2442 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 392 2.70 - 3.25: 13732 3.25 - 3.80: 21699 3.80 - 4.35: 29592 4.35 - 4.90: 49961 Nonbonded interactions: 115376 Sorted by model distance: nonbonded pdb=" OD1 ASN B 171 " pdb=" OG1 THR B 173 " model vdw 2.149 3.040 nonbonded pdb=" N GLN A 183 " pdb=" OE1 GLN A 183 " model vdw 2.234 3.120 nonbonded pdb=" O TYR I 50 " pdb=" OG SER I 54 " model vdw 2.236 3.040 nonbonded pdb=" OD1 ASN A 114 " pdb=" NE2 GLN A 226 " model vdw 2.252 3.120 nonbonded pdb=" OG SER B 93 " pdb=" ND1 HIS B 99 " model vdw 2.258 3.120 ... (remaining 115371 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'P' selection = chain 'V' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.590 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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 : 0.003 0.039 14652 Z= 0.142 Angle : 0.641 13.105 19911 Z= 0.318 Chirality : 0.045 0.438 2277 Planarity : 0.004 0.045 2421 Dihedral : 16.832 110.179 5910 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.20), residues: 1689 helix: -1.23 (0.26), residues: 357 sheet: -0.82 (0.27), residues: 396 loop : -0.63 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 89 TYR 0.029 0.001 TYR B 203 PHE 0.021 0.002 PHE G 72 TRP 0.018 0.001 TRP c 270 HIS 0.004 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00326 (14580) covalent geometry : angle 0.59904 (19722) SS BOND : bond 0.00435 ( 27) SS BOND : angle 1.29326 ( 54) hydrogen bonds : bond 0.26223 ( 496) hydrogen bonds : angle 9.85339 ( 1308) link_BETA1-4 : bond 0.00444 ( 21) link_BETA1-4 : angle 1.59817 ( 63) link_NAG-ASN : bond 0.00587 ( 24) link_NAG-ASN : angle 3.41990 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 24 ARG cc_start: 0.8207 (tpp80) cc_final: 0.7958 (mmm-85) REVERT: E 108 ILE cc_start: 0.7372 (mp) cc_final: 0.7135 (mp) REVERT: B 253 SER cc_start: 0.8323 (m) cc_final: 0.8049 (t) REVERT: H 88 LEU cc_start: 0.8730 (mt) cc_final: 0.8356 (mt) REVERT: H 95 ILE cc_start: 0.7898 (pt) cc_final: 0.7683 (pt) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.1290 time to fit residues: 55.4298 Evaluate side-chains 214 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.0770 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0370 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 308 ASN b 348 ASN J 36 ASN ** c 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.084411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.067743 restraints weight = 35753.908| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.15 r_work: 0.3027 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14652 Z= 0.133 Angle : 0.663 12.655 19911 Z= 0.330 Chirality : 0.046 0.397 2277 Planarity : 0.004 0.039 2421 Dihedral : 12.756 96.049 2820 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.00 % Allowed : 7.60 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.20), residues: 1689 helix: -0.15 (0.26), residues: 375 sheet: -0.76 (0.25), residues: 432 loop : -0.72 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 150 TYR 0.017 0.001 TYR F 96 PHE 0.016 0.001 PHE a 299 TRP 0.024 0.002 TRP a 289 HIS 0.004 0.001 HIS b 404 Details of bonding type rmsd covalent geometry : bond 0.00286 (14580) covalent geometry : angle 0.62694 (19722) SS BOND : bond 0.00434 ( 27) SS BOND : angle 1.19985 ( 54) hydrogen bonds : bond 0.04746 ( 496) hydrogen bonds : angle 6.32536 ( 1308) link_BETA1-4 : bond 0.00417 ( 21) link_BETA1-4 : angle 1.93796 ( 63) link_NAG-ASN : bond 0.00500 ( 24) link_NAG-ASN : angle 3.10634 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 232 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 72 TYR cc_start: 0.8337 (m-80) cc_final: 0.8089 (m-80) REVERT: E 107 GLU cc_start: 0.4688 (tm-30) cc_final: 0.4474 (tm-30) REVERT: a 292 LEU cc_start: 0.8923 (tp) cc_final: 0.8694 (tp) REVERT: B 253 SER cc_start: 0.8853 (m) cc_final: 0.8405 (t) REVERT: H 88 LEU cc_start: 0.9287 (mt) cc_final: 0.8736 (mt) REVERT: H 111 MET cc_start: 0.8647 (mtt) cc_final: 0.8169 (mtt) outliers start: 15 outliers final: 9 residues processed: 239 average time/residue: 0.1059 time to fit residues: 39.2725 Evaluate side-chains 221 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 212 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain b residue 309 VAL Chi-restraints excluded: chain b residue 337 GLU Chi-restraints excluded: chain b residue 394 VAL Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain J residue 29 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 41 optimal weight: 8.9990 chunk 162 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 238 HIS F 107 GLN a 348 ASN a 359 ASN G 27 GLN b 308 ASN C 169 GLN c 396 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.079221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.062845 restraints weight = 36804.363| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.11 r_work: 0.2912 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 14652 Z= 0.291 Angle : 0.742 16.047 19911 Z= 0.364 Chirality : 0.049 0.453 2277 Planarity : 0.004 0.046 2421 Dihedral : 11.325 97.403 2820 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.00 % Allowed : 9.67 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.20), residues: 1689 helix: -0.06 (0.26), residues: 384 sheet: -0.78 (0.25), residues: 435 loop : -0.84 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 150 TYR 0.019 0.002 TYR I 33 PHE 0.016 0.002 PHE G 72 TRP 0.023 0.002 TRP c 270 HIS 0.007 0.002 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00675 (14580) covalent geometry : angle 0.70276 (19722) SS BOND : bond 0.00485 ( 27) SS BOND : angle 1.27255 ( 54) hydrogen bonds : bond 0.04981 ( 496) hydrogen bonds : angle 5.84309 ( 1308) link_BETA1-4 : bond 0.00356 ( 21) link_BETA1-4 : angle 2.03945 ( 63) link_NAG-ASN : bond 0.00593 ( 24) link_NAG-ASN : angle 3.46659 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: a 292 LEU cc_start: 0.8963 (tp) cc_final: 0.8708 (tp) REVERT: H 88 LEU cc_start: 0.9335 (mt) cc_final: 0.9045 (mt) REVERT: H 111 MET cc_start: 0.8769 (mtt) cc_final: 0.8345 (mtt) REVERT: C 255 GLU cc_start: 0.7188 (tp30) cc_final: 0.6858 (mm-30) REVERT: J 111 MET cc_start: 0.8922 (mtt) cc_final: 0.8460 (mtt) REVERT: c 402 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8462 (tm-30) outliers start: 30 outliers final: 16 residues processed: 230 average time/residue: 0.1012 time to fit residues: 36.4017 Evaluate side-chains 220 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain a residue 287 THR Chi-restraints excluded: chain a residue 309 VAL Chi-restraints excluded: chain a residue 394 VAL Chi-restraints excluded: chain a residue 411 GLN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain b residue 309 VAL Chi-restraints excluded: chain b residue 394 VAL Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain J residue 29 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 71 optimal weight: 0.8980 chunk 14 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 38 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 62 optimal weight: 0.0270 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 36 ASN F 107 GLN B 254 GLN b 359 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.082615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.066254 restraints weight = 35833.480| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.10 r_work: 0.2995 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14652 Z= 0.107 Angle : 0.596 14.014 19911 Z= 0.295 Chirality : 0.044 0.435 2277 Planarity : 0.003 0.044 2421 Dihedral : 9.815 93.304 2820 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.07 % Allowed : 10.33 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.20), residues: 1689 helix: 0.46 (0.27), residues: 384 sheet: -0.66 (0.25), residues: 429 loop : -0.75 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 196 TYR 0.020 0.001 TYR I 50 PHE 0.012 0.001 PHE I 72 TRP 0.020 0.001 TRP a 289 HIS 0.006 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00232 (14580) covalent geometry : angle 0.55507 (19722) SS BOND : bond 0.00509 ( 27) SS BOND : angle 1.00850 ( 54) hydrogen bonds : bond 0.03418 ( 496) hydrogen bonds : angle 5.39957 ( 1308) link_BETA1-4 : bond 0.00513 ( 21) link_BETA1-4 : angle 1.90892 ( 63) link_NAG-ASN : bond 0.00449 ( 24) link_NAG-ASN : angle 3.13413 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 221 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 84 GLN cc_start: 0.8588 (tp40) cc_final: 0.8294 (tp40) REVERT: F 107 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8443 (pm20) REVERT: a 292 LEU cc_start: 0.8968 (tp) cc_final: 0.8745 (tp) REVERT: a 299 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7578 (m-80) REVERT: a 416 MET cc_start: 0.8320 (mmm) cc_final: 0.8028 (mmm) REVERT: B 131 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7786 (mmtt) REVERT: B 196 ARG cc_start: 0.8796 (ttp-170) cc_final: 0.8548 (ttp-110) REVERT: H 88 LEU cc_start: 0.9311 (mt) cc_final: 0.9017 (mt) REVERT: H 111 MET cc_start: 0.8756 (mtt) cc_final: 0.8348 (mtt) REVERT: b 290 MET cc_start: 0.7943 (ttm) cc_final: 0.7687 (ttm) outliers start: 31 outliers final: 14 residues processed: 238 average time/residue: 0.1030 time to fit residues: 37.8790 Evaluate side-chains 222 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 205 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain a residue 299 PHE Chi-restraints excluded: chain a residue 309 VAL Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain c residue 299 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 138 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 101 optimal weight: 0.0980 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 95 optimal weight: 0.0040 chunk 3 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 overall best weight: 2.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 107 GLN b 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.079639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.063331 restraints weight = 36480.660| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.08 r_work: 0.2924 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 14652 Z= 0.245 Angle : 0.679 15.618 19911 Z= 0.333 Chirality : 0.047 0.438 2277 Planarity : 0.004 0.042 2421 Dihedral : 9.713 88.823 2820 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.80 % Allowed : 11.60 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.20), residues: 1689 helix: 0.58 (0.27), residues: 366 sheet: -0.71 (0.25), residues: 447 loop : -0.75 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 74 TYR 0.015 0.002 TYR I 50 PHE 0.012 0.002 PHE c 405 TRP 0.021 0.002 TRP b 270 HIS 0.007 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00567 (14580) covalent geometry : angle 0.64089 (19722) SS BOND : bond 0.00471 ( 27) SS BOND : angle 1.31889 ( 54) hydrogen bonds : bond 0.04111 ( 496) hydrogen bonds : angle 5.47991 ( 1308) link_BETA1-4 : bond 0.00380 ( 21) link_BETA1-4 : angle 2.01972 ( 63) link_NAG-ASN : bond 0.00591 ( 24) link_NAG-ASN : angle 3.20151 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: F 84 GLN cc_start: 0.8670 (tp40) cc_final: 0.8347 (tp40) REVERT: B 131 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7634 (mmtt) REVERT: H 88 LEU cc_start: 0.9357 (mt) cc_final: 0.9069 (mt) REVERT: H 111 MET cc_start: 0.8751 (mtt) cc_final: 0.8321 (mtt) REVERT: b 287 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.8083 (p) outliers start: 27 outliers final: 16 residues processed: 219 average time/residue: 0.1073 time to fit residues: 36.3209 Evaluate side-chains 216 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain a residue 309 VAL Chi-restraints excluded: chain a residue 394 VAL Chi-restraints excluded: chain a residue 411 GLN Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain b residue 287 THR Chi-restraints excluded: chain b residue 394 VAL Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain c residue 373 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 41 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 5 optimal weight: 0.0040 chunk 160 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.081020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.064656 restraints weight = 36031.892| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.09 r_work: 0.2957 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14652 Z= 0.145 Angle : 0.620 14.718 19911 Z= 0.305 Chirality : 0.045 0.445 2277 Planarity : 0.003 0.044 2421 Dihedral : 9.179 84.135 2820 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.07 % Allowed : 12.13 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.20), residues: 1689 helix: 0.48 (0.26), residues: 384 sheet: -0.70 (0.25), residues: 447 loop : -0.71 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 196 TYR 0.017 0.001 TYR I 50 PHE 0.011 0.001 PHE G 72 TRP 0.023 0.002 TRP b 270 HIS 0.007 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00332 (14580) covalent geometry : angle 0.58235 (19722) SS BOND : bond 0.00425 ( 27) SS BOND : angle 1.22576 ( 54) hydrogen bonds : bond 0.03492 ( 496) hydrogen bonds : angle 5.29231 ( 1308) link_BETA1-4 : bond 0.00402 ( 21) link_BETA1-4 : angle 2.00013 ( 63) link_NAG-ASN : bond 0.00398 ( 24) link_NAG-ASN : angle 2.96700 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: E 76 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7141 (mm) REVERT: F 79 GLN cc_start: 0.7871 (mt0) cc_final: 0.7399 (mm-40) REVERT: B 131 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7935 (mmtt) REVERT: H 88 LEU cc_start: 0.9370 (mt) cc_final: 0.9080 (mt) REVERT: H 111 MET cc_start: 0.8865 (mtt) cc_final: 0.8430 (mtt) REVERT: J 91 GLU cc_start: 0.8998 (tp30) cc_final: 0.8680 (tp30) REVERT: c 372 TYR cc_start: 0.8589 (m-80) cc_final: 0.8322 (m-80) REVERT: c 402 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8233 (tm-30) outliers start: 31 outliers final: 19 residues processed: 229 average time/residue: 0.1104 time to fit residues: 38.8414 Evaluate side-chains 226 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain a residue 309 VAL Chi-restraints excluded: chain a residue 394 VAL Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain b residue 289 TRP Chi-restraints excluded: chain b residue 299 PHE Chi-restraints excluded: chain b residue 309 VAL Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain c residue 299 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 2 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 141 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 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 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.080661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.064346 restraints weight = 36214.858| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.09 r_work: 0.2949 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14652 Z= 0.158 Angle : 0.629 14.849 19911 Z= 0.308 Chirality : 0.045 0.452 2277 Planarity : 0.003 0.043 2421 Dihedral : 8.818 78.937 2820 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.07 % Allowed : 13.07 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.20), residues: 1689 helix: 0.80 (0.27), residues: 366 sheet: -0.69 (0.25), residues: 465 loop : -0.65 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 196 TYR 0.017 0.001 TYR B 72 PHE 0.011 0.001 PHE G 72 TRP 0.028 0.002 TRP b 270 HIS 0.007 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00366 (14580) covalent geometry : angle 0.59136 (19722) SS BOND : bond 0.00427 ( 27) SS BOND : angle 1.17519 ( 54) hydrogen bonds : bond 0.03489 ( 496) hydrogen bonds : angle 5.20367 ( 1308) link_BETA1-4 : bond 0.00376 ( 21) link_BETA1-4 : angle 2.09217 ( 63) link_NAG-ASN : bond 0.00364 ( 24) link_NAG-ASN : angle 2.95576 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: E 76 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.7091 (mm) REVERT: F 79 GLN cc_start: 0.7926 (mt0) cc_final: 0.7695 (mm-40) REVERT: B 131 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7962 (mmtt) REVERT: H 88 LEU cc_start: 0.9345 (mt) cc_final: 0.9060 (mt) REVERT: H 111 MET cc_start: 0.8861 (mtt) cc_final: 0.8404 (mtt) REVERT: J 91 GLU cc_start: 0.8988 (tp30) cc_final: 0.8675 (tp30) REVERT: c 372 TYR cc_start: 0.8634 (m-80) cc_final: 0.8400 (m-80) outliers start: 31 outliers final: 23 residues processed: 228 average time/residue: 0.1089 time to fit residues: 38.4853 Evaluate side-chains 229 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain a residue 309 VAL Chi-restraints excluded: chain a residue 314 GLU Chi-restraints excluded: chain a residue 394 VAL Chi-restraints excluded: chain a residue 411 GLN Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain b residue 289 TRP Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 107 GLN Chi-restraints excluded: chain c residue 299 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 13 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 125 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.081603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.065298 restraints weight = 35778.416| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.08 r_work: 0.2973 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14652 Z= 0.125 Angle : 0.615 14.441 19911 Z= 0.301 Chirality : 0.044 0.459 2277 Planarity : 0.003 0.043 2421 Dihedral : 8.353 73.187 2820 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.00 % Allowed : 13.27 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.20), residues: 1689 helix: 0.92 (0.27), residues: 366 sheet: -0.61 (0.25), residues: 465 loop : -0.62 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 196 TYR 0.016 0.001 TYR I 50 PHE 0.012 0.001 PHE b 299 TRP 0.030 0.002 TRP b 270 HIS 0.007 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00288 (14580) covalent geometry : angle 0.57924 (19722) SS BOND : bond 0.00370 ( 27) SS BOND : angle 1.10621 ( 54) hydrogen bonds : bond 0.03203 ( 496) hydrogen bonds : angle 5.10549 ( 1308) link_BETA1-4 : bond 0.00429 ( 21) link_BETA1-4 : angle 2.12670 ( 63) link_NAG-ASN : bond 0.00341 ( 24) link_NAG-ASN : angle 2.82463 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: E 76 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.7031 (mm) REVERT: F 84 GLN cc_start: 0.8635 (tp40) cc_final: 0.8328 (tp40) REVERT: F 91 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8279 (tp30) REVERT: B 131 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8046 (mmtt) REVERT: H 35 MET cc_start: 0.7680 (ptp) cc_final: 0.7341 (ptp) REVERT: H 88 LEU cc_start: 0.9334 (mt) cc_final: 0.9053 (mt) REVERT: H 111 MET cc_start: 0.8764 (mtt) cc_final: 0.8331 (mtt) REVERT: J 91 GLU cc_start: 0.9018 (tp30) cc_final: 0.8683 (tp30) REVERT: c 372 TYR cc_start: 0.8590 (m-80) cc_final: 0.8387 (m-80) outliers start: 30 outliers final: 23 residues processed: 228 average time/residue: 0.1094 time to fit residues: 38.4634 Evaluate side-chains 231 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain a residue 309 VAL Chi-restraints excluded: chain a residue 314 GLU Chi-restraints excluded: chain a residue 394 VAL Chi-restraints excluded: chain a residue 411 GLN Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 373 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 52 optimal weight: 4.9990 chunk 6 optimal weight: 0.0570 chunk 154 optimal weight: 0.1980 chunk 114 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.082500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.066345 restraints weight = 36070.416| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.08 r_work: 0.3004 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14652 Z= 0.111 Angle : 0.612 14.128 19911 Z= 0.299 Chirality : 0.044 0.463 2277 Planarity : 0.003 0.043 2421 Dihedral : 7.945 67.841 2820 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.87 % Allowed : 14.00 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.20), residues: 1689 helix: 0.76 (0.27), residues: 384 sheet: -0.46 (0.25), residues: 441 loop : -0.63 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 32 TYR 0.016 0.001 TYR I 50 PHE 0.011 0.001 PHE C 74 TRP 0.042 0.002 TRP b 289 HIS 0.006 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00254 (14580) covalent geometry : angle 0.57675 (19722) SS BOND : bond 0.00362 ( 27) SS BOND : angle 1.04956 ( 54) hydrogen bonds : bond 0.02989 ( 496) hydrogen bonds : angle 5.01314 ( 1308) link_BETA1-4 : bond 0.00460 ( 21) link_BETA1-4 : angle 2.18673 ( 63) link_NAG-ASN : bond 0.00340 ( 24) link_NAG-ASN : angle 2.71461 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: F 84 GLN cc_start: 0.8578 (tp40) cc_final: 0.8213 (tp40) REVERT: B 131 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.8050 (mmtt) REVERT: B 253 SER cc_start: 0.8938 (m) cc_final: 0.8482 (t) REVERT: H 88 LEU cc_start: 0.9309 (mt) cc_final: 0.9031 (mt) REVERT: H 111 MET cc_start: 0.8675 (mtt) cc_final: 0.8233 (mtt) REVERT: J 91 GLU cc_start: 0.9050 (tp30) cc_final: 0.8726 (tp30) outliers start: 28 outliers final: 21 residues processed: 227 average time/residue: 0.1131 time to fit residues: 39.4292 Evaluate side-chains 227 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain a residue 309 VAL Chi-restraints excluded: chain a residue 314 GLU Chi-restraints excluded: chain a residue 394 VAL Chi-restraints excluded: chain a residue 411 GLN Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 373 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 130 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 152 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 308 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.080834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.064584 restraints weight = 36403.532| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.10 r_work: 0.2961 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14652 Z= 0.172 Angle : 0.658 15.143 19911 Z= 0.321 Chirality : 0.045 0.493 2277 Planarity : 0.003 0.041 2421 Dihedral : 7.912 61.943 2820 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.60 % Allowed : 14.33 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.20), residues: 1689 helix: 0.61 (0.27), residues: 387 sheet: -0.49 (0.25), residues: 441 loop : -0.65 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 196 TYR 0.021 0.001 TYR B 100 PHE 0.021 0.001 PHE b 299 TRP 0.038 0.002 TRP b 289 HIS 0.006 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00400 (14580) covalent geometry : angle 0.62190 (19722) SS BOND : bond 0.00458 ( 27) SS BOND : angle 1.13230 ( 54) hydrogen bonds : bond 0.03446 ( 496) hydrogen bonds : angle 5.07547 ( 1308) link_BETA1-4 : bond 0.00357 ( 21) link_BETA1-4 : angle 2.24109 ( 63) link_NAG-ASN : bond 0.00341 ( 24) link_NAG-ASN : angle 2.93030 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.549 Fit side-chains REVERT: F 78 LYS cc_start: 0.8941 (mtmt) cc_final: 0.8678 (mtmm) REVERT: F 84 GLN cc_start: 0.8587 (tp40) cc_final: 0.8209 (tp40) REVERT: a 416 MET cc_start: 0.8518 (mmm) cc_final: 0.8012 (mmm) REVERT: B 131 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8080 (mmtt) REVERT: H 35 MET cc_start: 0.7656 (ptp) cc_final: 0.7312 (ptp) REVERT: H 88 LEU cc_start: 0.9334 (mt) cc_final: 0.9058 (mt) REVERT: H 111 MET cc_start: 0.8692 (mtt) cc_final: 0.8233 (mtt) REVERT: J 91 GLU cc_start: 0.9000 (tp30) cc_final: 0.8692 (tp30) outliers start: 24 outliers final: 22 residues processed: 215 average time/residue: 0.1095 time to fit residues: 36.2734 Evaluate side-chains 227 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain a residue 299 PHE Chi-restraints excluded: chain a residue 309 VAL Chi-restraints excluded: chain a residue 394 VAL Chi-restraints excluded: chain a residue 411 GLN Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 373 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 23 optimal weight: 0.1980 chunk 59 optimal weight: 5.9990 chunk 69 optimal weight: 0.1980 chunk 120 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 14 optimal weight: 0.0980 chunk 58 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.082118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.065962 restraints weight = 35981.555| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.06 r_work: 0.2996 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14652 Z= 0.117 Angle : 0.621 14.751 19911 Z= 0.303 Chirality : 0.044 0.491 2277 Planarity : 0.003 0.041 2421 Dihedral : 7.578 58.173 2820 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.87 % Allowed : 14.27 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.20), residues: 1689 helix: 0.79 (0.27), residues: 384 sheet: -0.24 (0.27), residues: 405 loop : -0.70 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 74 TYR 0.016 0.001 TYR B 100 PHE 0.016 0.001 PHE b 299 TRP 0.048 0.002 TRP b 289 HIS 0.006 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00269 (14580) covalent geometry : angle 0.58526 (19722) SS BOND : bond 0.00373 ( 27) SS BOND : angle 1.04663 ( 54) hydrogen bonds : bond 0.03057 ( 496) hydrogen bonds : angle 4.99949 ( 1308) link_BETA1-4 : bond 0.00432 ( 21) link_BETA1-4 : angle 2.20756 ( 63) link_NAG-ASN : bond 0.00324 ( 24) link_NAG-ASN : angle 2.78752 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3208.91 seconds wall clock time: 56 minutes 4.08 seconds (3364.08 seconds total)