Starting phenix.real_space_refine on Fri Jul 3 12:58:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dmh_27538/07_2026/8dmh_27538.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmh_27538/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dmh_27538/07_2026/8dmh_27538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmh_27538/07_2026/8dmh_27538.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dmh_27538/07_2026/8dmh_27538.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dmh_27538/07_2026/8dmh_27538.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dmh_27538/07_2026/8dmh_27538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmh_27538/07_2026/8dmh_27538.cif" } 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-6108/lib/python3.11/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 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 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 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 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 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 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 chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 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 chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 2.99, per 1000 atoms: 0.21 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: 1.40 Conformation dependent library (CDL) restraints added in 687.5 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: 0.42 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: 2.08 Time building geometry restraints manager: 1.81 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 - 17.95: 7407 17.95 - 35.91: 712 35.91 - 53.86: 82 53.86 - 71.81: 37 71.81 - 89.77: 12 Dihedral angle restraints: 8250 sinusoidal: 3255 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 8247 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.900 Find NCS groups from input model: 0.340 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 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 : 14.091 87.414 4971 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/Z covalent geometry : bond 0.00326 / 0.14 (14580) covalent geometry : angle 0.59904 / 0.31 (19722) SS BOND : bond 0.00435 / 0.23 ( 27) SS BOND : angle 1.29326 / 1.00 ( 54) hydrogen bonds : bond 0.26223 / 17.41 ( 496) hydrogen bonds : angle 9.85339 / 6.94 ( 1308) link_BETA1-4 : bond 0.00444 / 0.32 ( 21) link_BETA1-4 : angle 1.59817 / 1.03 ( 63) link_NAG-ASN : bond 0.00587 / 0.34 ( 24) link_NAG-ASN : angle 3.41990 / 2.14 ( 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 : 0.414 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: 0.1153 time to fit residues: 49.5918 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 : 0.325 ------------------------------------------------------------------------------- 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... ** F 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 308 ASN a 348 ASN b 348 ASN J 36 ASN ** c 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.084515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.067857 restraints weight = 35763.511| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.14 r_work: 0.3030 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1678 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= 0.126 Angle : 0.640 13.068 19911 Z= 0.324 Chirality : 0.045 0.441 2277 Planarity : 0.004 0.037 2421 Dihedral : 4.778 23.799 1881 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % 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: -0.14 (0.26), residues: 375 sheet: -0.77 (0.25), residues: 432 loop : -0.73 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 150 TYR 0.018 0.001 TYR F 96 PHE 0.017 0.001 PHE a 299 TRP 0.023 0.001 TRP a 289 HIS 0.004 0.001 HIS b 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (14580) covalent geometry : angle 0.60664 / 0.32 (19722) SS BOND : bond 0.00445 / 0.22 ( 27) SS BOND : angle 1.21157 / 0.90 ( 54) hydrogen bonds : bond 0.04383 / 3.01 ( 496) hydrogen bonds : angle 6.25126 / 4.39 ( 1308) link_BETA1-4 : bond 0.00404 / 0.28 ( 21) link_BETA1-4 : angle 1.45097 / 0.95 ( 63) link_NAG-ASN : bond 0.00505 / 0.29 ( 24) link_NAG-ASN : angle 3.09231 / 2.05 ( 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 251 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 236 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: a 292 LEU cc_start: 0.8923 (tp) cc_final: 0.8681 (tp) REVERT: B 253 SER cc_start: 0.8846 (m) cc_final: 0.8403 (t) REVERT: H 88 LEU cc_start: 0.9287 (mt) cc_final: 0.8736 (mt) REVERT: H 111 MET cc_start: 0.8708 (mtt) cc_final: 0.8302 (mtt) outliers start: 15 outliers final: 8 residues processed: 242 average time/residue: 0.0888 time to fit residues: 33.2596 Evaluate side-chains 222 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 214 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 162 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 GLN A 238 HIS a 359 ASN G 27 GLN b 308 ASN C 169 GLN c 396 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.078748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.062413 restraints weight = 36895.029| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.10 r_work: 0.2903 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 14652 Z= 0.310 Angle : 0.740 16.215 19911 Z= 0.367 Chirality : 0.049 0.472 2277 Planarity : 0.004 0.043 2421 Dihedral : 5.113 25.691 1881 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.27 % Allowed : 9.27 % Favored : 88.47 % 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: -1.09 (0.20), residues: 1689 helix: -0.11 (0.26), residues: 384 sheet: -0.81 (0.25), residues: 435 loop : -0.87 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 74 TYR 0.020 0.002 TYR I 33 PHE 0.017 0.002 PHE G 72 TRP 0.024 0.002 TRP c 270 HIS 0.007 0.002 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00716 / 0.31 (14580) covalent geometry : angle 0.70540 / 0.36 (19722) SS BOND : bond 0.00493 / 0.28 ( 27) SS BOND : angle 1.27899 / 0.90 ( 54) hydrogen bonds : bond 0.05062 / 3.39 ( 496) hydrogen bonds : angle 5.85608 / 4.10 ( 1308) link_BETA1-4 : bond 0.00345 / 0.24 ( 21) link_BETA1-4 : angle 1.74985 / 1.16 ( 63) link_NAG-ASN : bond 0.00625 / 0.36 ( 24) link_NAG-ASN : angle 3.34839 / 2.28 ( 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 243 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: a 292 LEU cc_start: 0.8969 (tp) cc_final: 0.8712 (tp) REVERT: B 131 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7720 (mmtt) REVERT: H 88 LEU cc_start: 0.9333 (mt) cc_final: 0.9042 (mt) REVERT: H 111 MET cc_start: 0.8761 (mtt) cc_final: 0.8360 (mtt) REVERT: C 109 GLU cc_start: 0.8417 (tt0) cc_final: 0.8074 (tt0) REVERT: C 255 GLU cc_start: 0.7095 (tp30) cc_final: 0.6694 (mm-30) REVERT: J 111 MET cc_start: 0.8870 (mtt) cc_final: 0.8557 (mtt) REVERT: c 402 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8464 (tm-30) outliers start: 34 outliers final: 17 residues processed: 231 average time/residue: 0.0994 time to fit residues: 36.0018 Evaluate side-chains 221 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER 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 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 131 LYS 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 C residue 131 LYS 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: 4.9990 chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 107 GLN B 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.081398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.065061 restraints weight = 36002.245| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.10 r_work: 0.2963 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14652 Z= 0.129 Angle : 0.594 13.983 19911 Z= 0.297 Chirality : 0.044 0.453 2277 Planarity : 0.004 0.050 2421 Dihedral : 4.797 23.539 1881 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.07 % Allowed : 10.80 % Favored : 87.13 % 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: -0.80 (0.20), residues: 1689 helix: 0.38 (0.27), residues: 384 sheet: -0.71 (0.25), residues: 429 loop : -0.77 (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 0.013 0.001 PHE G 72 TRP 0.019 0.001 TRP a 289 HIS 0.006 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (14580) covalent geometry : angle 0.56266 / 0.29 (19722) SS BOND : bond 0.00399 / 0.18 ( 27) SS BOND : angle 1.04974 / 0.67 ( 54) hydrogen bonds : bond 0.03624 / 2.48 ( 496) hydrogen bonds : angle 5.42355 / 3.80 ( 1308) link_BETA1-4 : bond 0.00416 / 0.30 ( 21) link_BETA1-4 : angle 1.44545 / 0.93 ( 63) link_NAG-ASN : bond 0.00403 / 0.24 ( 24) link_NAG-ASN : angle 2.83534 / 1.90 ( 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 245 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 84 GLN cc_start: 0.8686 (tp40) cc_final: 0.8416 (tp40) REVERT: F 91 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8635 (mm-30) REVERT: a 292 LEU cc_start: 0.8981 (tp) cc_final: 0.8748 (tp) REVERT: a 299 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: a 416 MET cc_start: 0.8333 (mmm) cc_final: 0.8064 (mmm) REVERT: B 131 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7860 (mmtt) REVERT: H 88 LEU cc_start: 0.9339 (mt) cc_final: 0.9042 (mt) REVERT: H 111 MET cc_start: 0.8751 (mtt) cc_final: 0.8362 (mtt) REVERT: b 290 MET cc_start: 0.7954 (ttm) cc_final: 0.7695 (ttm) REVERT: C 109 GLU cc_start: 0.8364 (tt0) cc_final: 0.8041 (tt0) REVERT: c 372 TYR cc_start: 0.8474 (m-80) cc_final: 0.8217 (m-80) outliers start: 31 outliers final: 15 residues processed: 230 average time/residue: 0.0984 time to fit residues: 35.1322 Evaluate side-chains 221 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER 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 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 J residue 29 THR 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: 0.6980 chunk 83 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 chunk 3 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.080260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.063965 restraints weight = 36271.698| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.09 r_work: 0.2939 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14652 Z= 0.190 Angle : 0.624 14.472 19911 Z= 0.310 Chirality : 0.045 0.455 2277 Planarity : 0.004 0.048 2421 Dihedral : 4.832 24.242 1881 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.80 % Allowed : 11.73 % Favored : 86.47 % 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: -0.78 (0.20), residues: 1689 helix: 0.39 (0.26), residues: 384 sheet: -0.72 (0.25), residues: 447 loop : -0.73 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 74 TYR 0.016 0.001 TYR I 50 PHE 0.012 0.001 PHE G 72 TRP 0.022 0.002 TRP b 270 HIS 0.007 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (14580) covalent geometry : angle 0.59384 / 0.30 (19722) SS BOND : bond 0.00420 / 0.23 ( 27) SS BOND : angle 1.21313 / 0.88 ( 54) hydrogen bonds : bond 0.03818 / 2.58 ( 496) hydrogen bonds : angle 5.43344 / 3.80 ( 1308) link_BETA1-4 : bond 0.00378 / 0.26 ( 21) link_BETA1-4 : angle 1.57225 / 1.01 ( 63) link_NAG-ASN : bond 0.00405 / 0.23 ( 24) link_NAG-ASN : angle 2.78405 / 1.89 ( 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 233 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: F 84 GLN cc_start: 0.8674 (tp40) cc_final: 0.8399 (tp40) REVERT: a 299 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.7950 (m-80) REVERT: B 131 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7874 (mmtt) REVERT: H 88 LEU cc_start: 0.9375 (mt) cc_final: 0.9086 (mt) REVERT: H 111 MET cc_start: 0.8739 (mtt) cc_final: 0.8281 (mtt) REVERT: b 287 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8088 (p) REVERT: C 109 GLU cc_start: 0.8386 (tt0) cc_final: 0.8130 (tt0) outliers start: 27 outliers final: 20 residues processed: 221 average time/residue: 0.1025 time to fit residues: 35.1948 Evaluate side-chains 220 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 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 F residue 107 GLN 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 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 36 ASN 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 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 373 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 41 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 146 optimal weight: 0.0370 chunk 132 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.080383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.064155 restraints weight = 36193.405| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.08 r_work: 0.2943 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14652 Z= 0.165 Angle : 0.609 14.186 19911 Z= 0.303 Chirality : 0.045 0.460 2277 Planarity : 0.003 0.045 2421 Dihedral : 4.762 24.084 1881 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.47 % Allowed : 11.93 % Favored : 85.60 % 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: -0.75 (0.20), residues: 1689 helix: 0.43 (0.26), residues: 384 sheet: -0.72 (0.25), residues: 447 loop : -0.72 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 20 TYR 0.016 0.001 TYR I 50 PHE 0.011 0.001 PHE G 72 TRP 0.025 0.002 TRP b 270 HIS 0.008 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (14580) covalent geometry : angle 0.57933 / 0.30 (19722) SS BOND : bond 0.00500 / 0.24 ( 27) SS BOND : angle 1.18542 / 0.82 ( 54) hydrogen bonds : bond 0.03603 / 2.44 ( 496) hydrogen bonds : angle 5.26593 / 3.68 ( 1308) link_BETA1-4 : bond 0.00362 / 0.27 ( 21) link_BETA1-4 : angle 1.53209 / 0.99 ( 63) link_NAG-ASN : bond 0.00407 / 0.23 ( 24) link_NAG-ASN : angle 2.72595 / 1.84 ( 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 242 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: F 79 GLN cc_start: 0.7930 (mt0) cc_final: 0.7657 (mm-40) REVERT: a 299 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.7959 (m-80) REVERT: B 131 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.8006 (mmtt) REVERT: H 88 LEU cc_start: 0.9384 (mt) cc_final: 0.9095 (mt) REVERT: H 111 MET cc_start: 0.8773 (mtt) cc_final: 0.8417 (mtt) REVERT: J 91 GLU cc_start: 0.8986 (tp30) cc_final: 0.8676 (tp30) REVERT: c 402 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8280 (tm-30) outliers start: 37 outliers final: 27 residues processed: 224 average time/residue: 0.1086 time to fit residues: 37.3859 Evaluate side-chains 228 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 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 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 107 GLN Chi-restraints excluded: chain b residue 289 TRP Chi-restraints excluded: chain b residue 309 VAL Chi-restraints excluded: chain b residue 394 VAL Chi-restraints excluded: chain C residue 103 MET 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 121 ILE Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 373 SER 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: 0.1980 chunk 87 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 141 optimal weight: 0.1980 chunk 58 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 107 GLN C 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.081820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.065493 restraints weight = 35875.772| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.08 r_work: 0.2979 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14652 Z= 0.113 Angle : 0.580 13.328 19911 Z= 0.290 Chirality : 0.044 0.449 2277 Planarity : 0.003 0.042 2421 Dihedral : 4.599 23.410 1881 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.00 % Allowed : 13.33 % Favored : 84.67 % 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: -0.63 (0.20), residues: 1689 helix: 0.61 (0.27), residues: 384 sheet: -0.67 (0.25), residues: 447 loop : -0.67 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 196 TYR 0.018 0.001 TYR B 72 PHE 0.011 0.001 PHE a 299 TRP 0.030 0.001 TRP b 270 HIS 0.007 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (14580) covalent geometry : angle 0.55313 / 0.28 (19722) SS BOND : bond 0.00416 / 0.20 ( 27) SS BOND : angle 1.09410 / 0.77 ( 54) hydrogen bonds : bond 0.03189 / 2.18 ( 496) hydrogen bonds : angle 5.09873 / 3.55 ( 1308) link_BETA1-4 : bond 0.00415 / 0.30 ( 21) link_BETA1-4 : angle 1.46143 / 0.94 ( 63) link_NAG-ASN : bond 0.00387 / 0.24 ( 24) link_NAG-ASN : angle 2.53382 / 1.70 ( 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 247 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: E 76 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.7020 (mm) REVERT: F 79 GLN cc_start: 0.7955 (mt0) cc_final: 0.7438 (mm-40) REVERT: a 299 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7774 (m-80) REVERT: H 35 MET cc_start: 0.7178 (mtm) cc_final: 0.6955 (ptp) REVERT: H 88 LEU cc_start: 0.9368 (mt) cc_final: 0.9076 (mt) REVERT: H 111 MET cc_start: 0.8766 (mtt) cc_final: 0.8353 (mtt) REVERT: J 91 GLU cc_start: 0.8994 (tp30) cc_final: 0.8675 (tp30) REVERT: c 402 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8202 (tm-30) outliers start: 30 outliers final: 20 residues processed: 232 average time/residue: 0.1043 time to fit residues: 37.3635 Evaluate side-chains 224 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 133 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain b residue 299 PHE 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 I residue 108 ILE Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 107 GLN Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 373 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 13 optimal weight: 0.0980 chunk 106 optimal weight: 0.1980 chunk 125 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 GLN I 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.082196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.065903 restraints weight = 35623.837| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.07 r_work: 0.2990 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14652 Z= 0.113 Angle : 0.577 13.055 19911 Z= 0.288 Chirality : 0.044 0.447 2277 Planarity : 0.003 0.040 2421 Dihedral : 4.503 23.175 1881 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.80 % Allowed : 13.87 % Favored : 84.33 % 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: -0.53 (0.20), residues: 1689 helix: 0.72 (0.27), residues: 384 sheet: -0.44 (0.26), residues: 411 loop : -0.73 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG a 422 TYR 0.016 0.001 TYR C 100 PHE 0.011 0.001 PHE a 299 TRP 0.037 0.002 TRP b 289 HIS 0.007 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (14580) covalent geometry : angle 0.55174 / 0.28 (19722) SS BOND : bond 0.00386 / 0.19 ( 27) SS BOND : angle 1.07652 / 0.76 ( 54) hydrogen bonds : bond 0.03105 / 2.14 ( 496) hydrogen bonds : angle 5.00471 / 3.49 ( 1308) link_BETA1-4 : bond 0.00425 / 0.31 ( 21) link_BETA1-4 : angle 1.45919 / 0.94 ( 63) link_NAG-ASN : bond 0.00370 / 0.24 ( 24) link_NAG-ASN : angle 2.44774 / 1.65 ( 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 238 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: F 79 GLN cc_start: 0.7969 (mt0) cc_final: 0.7513 (mm-40) REVERT: H 35 MET cc_start: 0.7267 (mtm) cc_final: 0.7007 (ptp) REVERT: H 88 LEU cc_start: 0.9353 (mt) cc_final: 0.9062 (mt) REVERT: H 111 MET cc_start: 0.8726 (mtt) cc_final: 0.8289 (mtt) REVERT: J 91 GLU cc_start: 0.9022 (tp30) cc_final: 0.8691 (tp30) REVERT: c 402 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8182 (tm-30) outliers start: 27 outliers final: 22 residues processed: 223 average time/residue: 0.1081 time to fit residues: 37.3430 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 : 0.654 ------------------------------------------------------------------------------- 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 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 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 394 VAL Chi-restraints excluded: chain C residue 73 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 J residue 29 THR Chi-restraints excluded: chain J residue 121 ILE 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: 0.9980 chunk 6 optimal weight: 0.7980 chunk 154 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.081989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.065646 restraints weight = 36156.055| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.10 r_work: 0.2986 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14652 Z= 0.125 Angle : 0.585 13.150 19911 Z= 0.292 Chirality : 0.044 0.448 2277 Planarity : 0.003 0.040 2421 Dihedral : 4.511 24.185 1881 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.93 % Allowed : 14.07 % Favored : 84.00 % 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: -0.54 (0.20), residues: 1689 helix: 0.67 (0.27), residues: 387 sheet: -0.44 (0.26), residues: 411 loop : -0.72 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 196 TYR 0.015 0.001 TYR I 50 PHE 0.012 0.001 PHE b 299 TRP 0.036 0.002 TRP b 270 HIS 0.007 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (14580) covalent geometry : angle 0.55993 / 0.29 (19722) SS BOND : bond 0.00491 / 0.30 ( 27) SS BOND : angle 1.10605 / 0.80 ( 54) hydrogen bonds : bond 0.03118 / 2.14 ( 496) hydrogen bonds : angle 5.02923 / 3.50 ( 1308) link_BETA1-4 : bond 0.00396 / 0.29 ( 21) link_BETA1-4 : angle 1.47410 / 0.95 ( 63) link_NAG-ASN : bond 0.00340 / 0.22 ( 24) link_NAG-ASN : angle 2.44755 / 1.66 ( 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 237 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: F 79 GLN cc_start: 0.8006 (mt0) cc_final: 0.7506 (mm-40) REVERT: H 88 LEU cc_start: 0.9340 (mt) cc_final: 0.9050 (mt) REVERT: H 111 MET cc_start: 0.8705 (mtt) cc_final: 0.8251 (mtt) REVERT: J 91 GLU cc_start: 0.9009 (tp30) cc_final: 0.8679 (tp30) REVERT: c 402 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8169 (tm-30) outliers start: 29 outliers final: 23 residues processed: 221 average time/residue: 0.1071 time to fit residues: 36.6338 Evaluate side-chains 226 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 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 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 314 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 I residue 108 ILE Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 121 ILE 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: 2.9990 chunk 131 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.080404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.064271 restraints weight = 36451.914| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.05 r_work: 0.2954 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14652 Z= 0.186 Angle : 0.637 14.045 19911 Z= 0.316 Chirality : 0.046 0.469 2277 Planarity : 0.003 0.037 2421 Dihedral : 4.671 26.037 1881 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.93 % Allowed : 13.93 % 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: -0.65 (0.20), residues: 1689 helix: 0.55 (0.27), residues: 387 sheet: -0.70 (0.25), residues: 447 loop : -0.64 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 74 TYR 0.025 0.001 TYR B 100 PHE 0.013 0.001 PHE b 299 TRP 0.040 0.002 TRP b 270 HIS 0.007 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (14580) covalent geometry : angle 0.60873 / 0.31 (19722) SS BOND : bond 0.00483 / 0.28 ( 27) SS BOND : angle 1.36695 / 1.04 ( 54) hydrogen bonds : bond 0.03527 / 2.38 ( 496) hydrogen bonds : angle 5.13385 / 3.58 ( 1308) link_BETA1-4 : bond 0.00334 / 0.25 ( 21) link_BETA1-4 : angle 1.59542 / 1.03 ( 63) link_NAG-ASN : bond 0.00410 / 0.23 ( 24) link_NAG-ASN : angle 2.64847 / 1.80 ( 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 234 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 0.561 Fit side-chains REVERT: G 80 GLU cc_start: 0.7722 (mp0) cc_final: 0.6997 (mp0) REVERT: H 88 LEU cc_start: 0.9383 (mt) cc_final: 0.9104 (mt) REVERT: H 111 MET cc_start: 0.8637 (mtt) cc_final: 0.8119 (mtt) REVERT: J 91 GLU cc_start: 0.9024 (tp30) cc_final: 0.8710 (tp30) REVERT: c 402 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8389 (tm-30) outliers start: 29 outliers final: 22 residues processed: 219 average time/residue: 0.1038 time to fit residues: 35.1517 Evaluate side-chains 225 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 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 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 107 GLN Chi-restraints excluded: chain b residue 394 VAL Chi-restraints excluded: chain C residue 73 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 J residue 29 THR Chi-restraints excluded: chain J residue 121 ILE 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: 0.0000 chunk 59 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 120 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 153 optimal weight: 0.0870 chunk 8 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 overall best weight: 0.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.082298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.066125 restraints weight = 35901.162| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.09 r_work: 0.2996 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 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 : 0.003 0.036 14652 Z= 0.111 Angle : 0.598 13.299 19911 Z= 0.297 Chirality : 0.044 0.454 2277 Planarity : 0.003 0.038 2421 Dihedral : 4.554 25.010 1881 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.40 % Allowed : 14.67 % Favored : 83.93 % 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: 0.76 (0.27), residues: 384 sheet: -0.49 (0.26), residues: 414 loop : -0.67 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 74 TYR 0.017 0.001 TYR I 50 PHE 0.014 0.001 PHE b 299 TRP 0.044 0.002 TRP b 289 HIS 0.006 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (14580) covalent geometry : angle 0.57270 / 0.29 (19722) SS BOND : bond 0.00421 / 0.22 ( 27) SS BOND : angle 1.15941 / 0.86 ( 54) hydrogen bonds : bond 0.03054 / 2.09 ( 496) hydrogen bonds : angle 5.04175 / 3.52 ( 1308) link_BETA1-4 : bond 0.00411 / 0.29 ( 21) link_BETA1-4 : angle 1.46526 / 0.94 ( 63) link_NAG-ASN : bond 0.00417 / 0.26 ( 24) link_NAG-ASN : angle 2.46019 / 1.66 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3102.50 seconds wall clock time: 54 minutes 21.88 seconds (3261.88 seconds total)