Starting phenix.real_space_refine on Tue Jul 7 05:36:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fgg_31580/07_2026/7fgg_31580.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fgg_31580/07_2026/7fgg_31580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fgg_31580/07_2026/7fgg_31580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fgg_31580/07_2026/7fgg_31580.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7fgg_31580/07_2026/7fgg_31580.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fgg_31580/07_2026/7fgg_31580.cif" model { file = "/net/cci-nas-00/data/ceres_data/7fgg_31580/07_2026/7fgg_31580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fgg_31580/07_2026/7fgg_31580.cif" } resolution = 2.19 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= 0.045 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: 7 Type Number sf(0) Gaussians Zn 12 6.06 5 P 36 5.49 5 Mg 12 5.21 5 S 348 5.16 5 C 27228 2.51 5 N 7584 2.21 5 O 9912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 192 residue(s): 0.05s 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: 45132 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3593 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Unusual residues: {' MG': 1, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "B" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "C" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "D" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "E" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "F" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "G" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "H" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "I" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "J" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "K" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "L" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1024 SG CYS A 134 160.681 36.869 62.044 1.00 0.00 S ATOM 1076 SG CYS A 141 157.732 34.016 61.465 1.00 0.00 S Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Residues with excluded nonbonded symmetry interactions: 24 residue: pdb=" N ACYS A 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 236 " occ=0.50 residue: pdb=" N AARG A 289 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 289 " occ=0.50 residue: pdb=" N ACYS B 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 236 " occ=0.50 residue: pdb=" N AARG B 289 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 289 " occ=0.50 residue: pdb=" N ACYS C 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 236 " occ=0.50 residue: pdb=" N AARG C 289 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 289 " occ=0.50 residue: pdb=" N ACYS D 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 236 " occ=0.50 residue: pdb=" N AARG D 289 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 289 " occ=0.50 residue: pdb=" N ACYS E 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS E 236 " occ=0.50 residue: pdb=" N AARG E 289 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG E 289 " occ=0.50 residue: pdb=" N ACYS F 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS F 236 " occ=0.50 residue: pdb=" N AARG F 289 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG F 289 " occ=0.50 ... (remaining 12 not shown) Time building chain proxies: 6.69, per 1000 atoms: 0.15 Number of scatterers: 45132 At special positions: 0 Unit cell: (206.55, 206.55, 90.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 12 29.99 S 348 16.00 P 36 15.00 Mg 12 11.99 O 9912 8.00 N 7584 7.00 C 27228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.34 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 141 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 134 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 79 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 141 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 134 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" NE2 HIS C 79 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 141 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 134 " pdb=" ZN D1001 " pdb="ZN ZN D1001 " - pdb=" NE2 HIS D 79 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 141 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 134 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 79 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 141 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 134 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" NE2 HIS F 79 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 141 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 134 " pdb=" ZN G1001 " pdb="ZN ZN G1001 " - pdb=" NE2 HIS G 79 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 141 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 134 " pdb=" ZN H1001 " pdb="ZN ZN H1001 " - pdb=" NE2 HIS H 79 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 141 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 134 " pdb=" ZN I1001 " pdb="ZN ZN I1001 " - pdb=" NE2 HIS I 79 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 141 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 134 " pdb=" ZN J1001 " pdb="ZN ZN J1001 " - pdb=" NE2 HIS J 79 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 141 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 134 " pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" NE2 HIS K 79 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 141 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 134 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" NE2 HIS L 79 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 141 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 134 " 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10344 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 48 sheets defined 35.9% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 removed outlier: 4.211A pdb=" N ALA A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 55 removed outlier: 3.596A pdb=" N ARG A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.728A pdb=" N MET A 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 103 removed outlier: 3.525A pdb=" N ARG A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.539A pdb=" N MET A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.829A pdb=" N TRP A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.621A pdb=" N LEU A 346 " --> pdb=" O THR A 343 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 348 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 364 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 404 Processing helix chain 'A' and resid 461 through 473 Processing helix chain 'B' and resid 13 through 22 removed outlier: 4.211A pdb=" N ALA B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 55 removed outlier: 3.596A pdb=" N ARG B 41 " --> pdb=" O HIS B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 72 removed outlier: 3.729A pdb=" N MET B 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 103 removed outlier: 3.525A pdb=" N ARG B 92 " --> pdb=" O GLU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 Processing helix chain 'B' and resid 157 through 167 Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.540A pdb=" N MET B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 252 through 258 removed outlier: 3.830A pdb=" N TRP B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 342 Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.620A pdb=" N LEU B 346 " --> pdb=" O THR B 343 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR B 348 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 364 Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 383 through 404 Processing helix chain 'B' and resid 461 through 473 Processing helix chain 'C' and resid 13 through 22 removed outlier: 4.212A pdb=" N ALA C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 55 removed outlier: 3.596A pdb=" N ARG C 41 " --> pdb=" O HIS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.728A pdb=" N MET C 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 103 removed outlier: 3.526A pdb=" N ARG C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'C' and resid 180 through 185 removed outlier: 3.540A pdb=" N MET C 184 " --> pdb=" O THR C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 252 through 258 removed outlier: 3.830A pdb=" N TRP C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 343 through 348 removed outlier: 3.621A pdb=" N LEU C 346 " --> pdb=" O THR C 343 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C 348 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 383 through 404 Processing helix chain 'C' and resid 461 through 473 Processing helix chain 'D' and resid 13 through 22 removed outlier: 4.211A pdb=" N ALA D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 55 removed outlier: 3.596A pdb=" N ARG D 41 " --> pdb=" O HIS D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 72 removed outlier: 3.728A pdb=" N MET D 72 " --> pdb=" O ALA D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 103 removed outlier: 3.525A pdb=" N ARG D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 125 Processing helix chain 'D' and resid 157 through 167 Processing helix chain 'D' and resid 180 through 185 removed outlier: 3.539A pdb=" N MET D 184 " --> pdb=" O THR D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 252 through 258 removed outlier: 3.829A pdb=" N TRP D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 343 through 348 removed outlier: 3.621A pdb=" N LEU D 346 " --> pdb=" O THR D 343 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR D 348 " --> pdb=" O ILE D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 364 Processing helix chain 'D' and resid 380 through 382 No H-bonds generated for 'chain 'D' and resid 380 through 382' Processing helix chain 'D' and resid 383 through 404 Processing helix chain 'D' and resid 461 through 473 Processing helix chain 'E' and resid 13 through 22 removed outlier: 4.212A pdb=" N ALA E 17 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 55 removed outlier: 3.596A pdb=" N ARG E 41 " --> pdb=" O HIS E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 72 removed outlier: 3.729A pdb=" N MET E 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 103 removed outlier: 3.525A pdb=" N ARG E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 125 Processing helix chain 'E' and resid 157 through 167 Processing helix chain 'E' and resid 180 through 185 removed outlier: 3.539A pdb=" N MET E 184 " --> pdb=" O THR E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 252 through 258 removed outlier: 3.829A pdb=" N TRP E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 342 Processing helix chain 'E' and resid 343 through 348 removed outlier: 3.620A pdb=" N LEU E 346 " --> pdb=" O THR E 343 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR E 348 " --> pdb=" O ILE E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 364 Processing helix chain 'E' and resid 380 through 382 No H-bonds generated for 'chain 'E' and resid 380 through 382' Processing helix chain 'E' and resid 383 through 404 Processing helix chain 'E' and resid 461 through 473 Processing helix chain 'F' and resid 13 through 22 removed outlier: 4.211A pdb=" N ALA F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 55 removed outlier: 3.596A pdb=" N ARG F 41 " --> pdb=" O HIS F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 72 removed outlier: 3.727A pdb=" N MET F 72 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 103 removed outlier: 3.525A pdb=" N ARG F 92 " --> pdb=" O GLU F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 125 Processing helix chain 'F' and resid 157 through 167 Processing helix chain 'F' and resid 180 through 185 removed outlier: 3.539A pdb=" N MET F 184 " --> pdb=" O THR F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 252 through 258 removed outlier: 3.829A pdb=" N TRP F 258 " --> pdb=" O LEU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 342 Processing helix chain 'F' and resid 343 through 348 removed outlier: 3.621A pdb=" N LEU F 346 " --> pdb=" O THR F 343 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR F 348 " --> pdb=" O ILE F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 364 Processing helix chain 'F' and resid 380 through 382 No H-bonds generated for 'chain 'F' and resid 380 through 382' Processing helix chain 'F' and resid 383 through 404 Processing helix chain 'F' and resid 461 through 473 Processing helix chain 'G' and resid 13 through 22 removed outlier: 4.211A pdb=" N ALA G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 55 removed outlier: 3.596A pdb=" N ARG G 41 " --> pdb=" O HIS G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 72 removed outlier: 3.728A pdb=" N MET G 72 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 103 removed outlier: 3.526A pdb=" N ARG G 92 " --> pdb=" O GLU G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 125 Processing helix chain 'G' and resid 157 through 167 Processing helix chain 'G' and resid 180 through 185 removed outlier: 3.539A pdb=" N MET G 184 " --> pdb=" O THR G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing helix chain 'G' and resid 252 through 258 removed outlier: 3.829A pdb=" N TRP G 258 " --> pdb=" O LEU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 342 Processing helix chain 'G' and resid 343 through 348 removed outlier: 3.621A pdb=" N LEU G 346 " --> pdb=" O THR G 343 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR G 348 " --> pdb=" O ILE G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 364 Processing helix chain 'G' and resid 380 through 382 No H-bonds generated for 'chain 'G' and resid 380 through 382' Processing helix chain 'G' and resid 383 through 404 Processing helix chain 'G' and resid 461 through 473 Processing helix chain 'H' and resid 13 through 22 removed outlier: 4.211A pdb=" N ALA H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 55 removed outlier: 3.596A pdb=" N ARG H 41 " --> pdb=" O HIS H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 72 removed outlier: 3.728A pdb=" N MET H 72 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 103 removed outlier: 3.526A pdb=" N ARG H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 Processing helix chain 'H' and resid 157 through 167 Processing helix chain 'H' and resid 180 through 185 removed outlier: 3.539A pdb=" N MET H 184 " --> pdb=" O THR H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 203 through 205 No H-bonds generated for 'chain 'H' and resid 203 through 205' Processing helix chain 'H' and resid 252 through 258 removed outlier: 3.830A pdb=" N TRP H 258 " --> pdb=" O LEU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 342 Processing helix chain 'H' and resid 343 through 348 removed outlier: 3.621A pdb=" N LEU H 346 " --> pdb=" O THR H 343 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR H 348 " --> pdb=" O ILE H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 351 through 364 Processing helix chain 'H' and resid 380 through 382 No H-bonds generated for 'chain 'H' and resid 380 through 382' Processing helix chain 'H' and resid 383 through 404 Processing helix chain 'H' and resid 461 through 473 Processing helix chain 'I' and resid 13 through 22 removed outlier: 4.210A pdb=" N ALA I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 55 removed outlier: 3.596A pdb=" N ARG I 41 " --> pdb=" O HIS I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 72 removed outlier: 3.727A pdb=" N MET I 72 " --> pdb=" O ALA I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 103 removed outlier: 3.525A pdb=" N ARG I 92 " --> pdb=" O GLU I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 125 Processing helix chain 'I' and resid 157 through 167 Processing helix chain 'I' and resid 180 through 185 removed outlier: 3.539A pdb=" N MET I 184 " --> pdb=" O THR I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 195 No H-bonds generated for 'chain 'I' and resid 193 through 195' Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 252 through 258 removed outlier: 3.830A pdb=" N TRP I 258 " --> pdb=" O LEU I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 342 Processing helix chain 'I' and resid 343 through 348 removed outlier: 3.621A pdb=" N LEU I 346 " --> pdb=" O THR I 343 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR I 348 " --> pdb=" O ILE I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 364 Processing helix chain 'I' and resid 380 through 382 No H-bonds generated for 'chain 'I' and resid 380 through 382' Processing helix chain 'I' and resid 383 through 404 Processing helix chain 'I' and resid 461 through 473 Processing helix chain 'J' and resid 13 through 22 removed outlier: 4.212A pdb=" N ALA J 17 " --> pdb=" O ALA J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 55 removed outlier: 3.596A pdb=" N ARG J 41 " --> pdb=" O HIS J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 3.727A pdb=" N MET J 72 " --> pdb=" O ALA J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 103 removed outlier: 3.526A pdb=" N ARG J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 125 Processing helix chain 'J' and resid 157 through 167 Processing helix chain 'J' and resid 180 through 185 removed outlier: 3.539A pdb=" N MET J 184 " --> pdb=" O THR J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 195 No H-bonds generated for 'chain 'J' and resid 193 through 195' Processing helix chain 'J' and resid 203 through 205 No H-bonds generated for 'chain 'J' and resid 203 through 205' Processing helix chain 'J' and resid 252 through 258 removed outlier: 3.829A pdb=" N TRP J 258 " --> pdb=" O LEU J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 342 Processing helix chain 'J' and resid 343 through 348 removed outlier: 3.621A pdb=" N LEU J 346 " --> pdb=" O THR J 343 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR J 348 " --> pdb=" O ILE J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 351 through 364 Processing helix chain 'J' and resid 380 through 382 No H-bonds generated for 'chain 'J' and resid 380 through 382' Processing helix chain 'J' and resid 383 through 404 Processing helix chain 'J' and resid 461 through 473 Processing helix chain 'K' and resid 13 through 22 removed outlier: 4.210A pdb=" N ALA K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 55 removed outlier: 3.596A pdb=" N ARG K 41 " --> pdb=" O HIS K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 72 removed outlier: 3.728A pdb=" N MET K 72 " --> pdb=" O ALA K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 103 removed outlier: 3.526A pdb=" N ARG K 92 " --> pdb=" O GLU K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 125 Processing helix chain 'K' and resid 157 through 167 Processing helix chain 'K' and resid 180 through 185 removed outlier: 3.539A pdb=" N MET K 184 " --> pdb=" O THR K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 193 through 195 No H-bonds generated for 'chain 'K' and resid 193 through 195' Processing helix chain 'K' and resid 203 through 205 No H-bonds generated for 'chain 'K' and resid 203 through 205' Processing helix chain 'K' and resid 252 through 258 removed outlier: 3.830A pdb=" N TRP K 258 " --> pdb=" O LEU K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 342 Processing helix chain 'K' and resid 343 through 348 removed outlier: 3.621A pdb=" N LEU K 346 " --> pdb=" O THR K 343 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR K 348 " --> pdb=" O ILE K 345 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 364 Processing helix chain 'K' and resid 380 through 382 No H-bonds generated for 'chain 'K' and resid 380 through 382' Processing helix chain 'K' and resid 383 through 404 Processing helix chain 'K' and resid 461 through 473 Processing helix chain 'L' and resid 13 through 22 removed outlier: 4.211A pdb=" N ALA L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 55 removed outlier: 3.596A pdb=" N ARG L 41 " --> pdb=" O HIS L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 72 removed outlier: 3.729A pdb=" N MET L 72 " --> pdb=" O ALA L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 103 removed outlier: 3.526A pdb=" N ARG L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 125 Processing helix chain 'L' and resid 157 through 167 Processing helix chain 'L' and resid 180 through 185 removed outlier: 3.539A pdb=" N MET L 184 " --> pdb=" O THR L 180 " (cutoff:3.500A) Processing helix chain 'L' and resid 193 through 195 No H-bonds generated for 'chain 'L' and resid 193 through 195' Processing helix chain 'L' and resid 203 through 205 No H-bonds generated for 'chain 'L' and resid 203 through 205' Processing helix chain 'L' and resid 252 through 258 removed outlier: 3.828A pdb=" N TRP L 258 " --> pdb=" O LEU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 335 through 342 Processing helix chain 'L' and resid 343 through 348 removed outlier: 3.621A pdb=" N LEU L 346 " --> pdb=" O THR L 343 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR L 348 " --> pdb=" O ILE L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 351 through 364 Processing helix chain 'L' and resid 380 through 382 No H-bonds generated for 'chain 'L' and resid 380 through 382' Processing helix chain 'L' and resid 383 through 404 Processing helix chain 'L' and resid 461 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134 removed outlier: 8.213A pdb=" N CYS A 134 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS A 80 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 147 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN A 151 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 280 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N AARG A 289 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N THR A 278 " --> pdb=" O AARG A 289 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR A 291 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N CYS A 276 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N SER A 293 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N CYS A 274 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 251 removed outlier: 3.638A pdb=" N THR A 197 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA A 189 " --> pdb=" O CYS A 331 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N TYR A 333 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ALA A 191 " --> pdb=" O TYR A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 307 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 133 through 134 removed outlier: 8.214A pdb=" N CYS B 134 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS B 80 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 147 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN B 151 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 280 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N AARG B 289 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N THR B 278 " --> pdb=" O AARG B 289 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N THR B 291 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N CYS B 276 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N SER B 293 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N CYS B 274 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 251 removed outlier: 3.639A pdb=" N THR B 197 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA B 189 " --> pdb=" O CYS B 331 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N TYR B 333 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ALA B 191 " --> pdb=" O TYR B 333 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 303 through 307 Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'C' and resid 133 through 134 removed outlier: 8.212A pdb=" N CYS C 134 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N CYS C 80 " --> pdb=" O CYS C 134 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 147 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN C 151 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 280 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N AARG C 289 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N THR C 278 " --> pdb=" O AARG C 289 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR C 291 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N CYS C 276 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER C 293 " --> pdb=" O CYS C 274 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N CYS C 274 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 246 through 251 removed outlier: 3.638A pdb=" N THR C 197 " --> pdb=" O TYR C 192 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ALA C 189 " --> pdb=" O CYS C 331 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N TYR C 333 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ALA C 191 " --> pdb=" O TYR C 333 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 303 through 307 Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'D' and resid 133 through 134 removed outlier: 8.212A pdb=" N CYS D 134 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS D 80 " --> pdb=" O CYS D 134 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL D 147 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN D 151 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL D 280 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N AARG D 289 " --> pdb=" O THR D 278 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N THR D 278 " --> pdb=" O AARG D 289 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N THR D 291 " --> pdb=" O CYS D 276 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N CYS D 276 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER D 293 " --> pdb=" O CYS D 274 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N CYS D 274 " --> pdb=" O SER D 293 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 246 through 251 removed outlier: 3.639A pdb=" N THR D 197 " --> pdb=" O TYR D 192 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ALA D 189 " --> pdb=" O CYS D 331 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N TYR D 333 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ALA D 191 " --> pdb=" O TYR D 333 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 303 through 307 Processing sheet with id=AB8, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'E' and resid 133 through 134 removed outlier: 8.213A pdb=" N CYS E 134 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS E 80 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL E 147 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLN E 151 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL E 280 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N AARG E 289 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N THR E 278 " --> pdb=" O AARG E 289 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N THR E 291 " --> pdb=" O CYS E 276 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N CYS E 276 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER E 293 " --> pdb=" O CYS E 274 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N CYS E 274 " --> pdb=" O SER E 293 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 246 through 251 removed outlier: 3.638A pdb=" N THR E 197 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA E 189 " --> pdb=" O CYS E 331 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N TYR E 333 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ALA E 191 " --> pdb=" O TYR E 333 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 303 through 307 Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AC4, first strand: chain 'F' and resid 133 through 134 removed outlier: 8.212A pdb=" N CYS F 134 " --> pdb=" O TYR F 78 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS F 80 " --> pdb=" O CYS F 134 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL F 147 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN F 151 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL F 280 " --> pdb=" O VAL F 287 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N AARG F 289 " --> pdb=" O THR F 278 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N THR F 278 " --> pdb=" O AARG F 289 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR F 291 " --> pdb=" O CYS F 276 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N CYS F 276 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER F 293 " --> pdb=" O CYS F 274 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N CYS F 274 " --> pdb=" O SER F 293 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 246 through 251 removed outlier: 3.638A pdb=" N THR F 197 " --> pdb=" O TYR F 192 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA F 189 " --> pdb=" O CYS F 331 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N TYR F 333 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ALA F 191 " --> pdb=" O TYR F 333 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 303 through 307 Processing sheet with id=AC7, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'G' and resid 133 through 134 removed outlier: 8.211A pdb=" N CYS G 134 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N CYS G 80 " --> pdb=" O CYS G 134 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL G 147 " --> pdb=" O THR G 60 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN G 151 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL G 280 " --> pdb=" O VAL G 287 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N AARG G 289 " --> pdb=" O THR G 278 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N THR G 278 " --> pdb=" O AARG G 289 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N THR G 291 " --> pdb=" O CYS G 276 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N CYS G 276 " --> pdb=" O THR G 291 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER G 293 " --> pdb=" O CYS G 274 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N CYS G 274 " --> pdb=" O SER G 293 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 246 through 251 removed outlier: 3.638A pdb=" N THR G 197 " --> pdb=" O TYR G 192 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ALA G 189 " --> pdb=" O CYS G 331 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N TYR G 333 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ALA G 191 " --> pdb=" O TYR G 333 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 303 through 307 Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'H' and resid 133 through 134 removed outlier: 8.212A pdb=" N CYS H 134 " --> pdb=" O TYR H 78 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS H 80 " --> pdb=" O CYS H 134 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL H 147 " --> pdb=" O THR H 60 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLN H 151 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL H 280 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N AARG H 289 " --> pdb=" O THR H 278 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N THR H 278 " --> pdb=" O AARG H 289 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR H 291 " --> pdb=" O CYS H 276 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N CYS H 276 " --> pdb=" O THR H 291 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER H 293 " --> pdb=" O CYS H 274 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N CYS H 274 " --> pdb=" O SER H 293 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 246 through 251 removed outlier: 3.638A pdb=" N THR H 197 " --> pdb=" O TYR H 192 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ALA H 189 " --> pdb=" O CYS H 331 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N TYR H 333 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ALA H 191 " --> pdb=" O TYR H 333 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 303 through 307 Processing sheet with id=AD6, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD7, first strand: chain 'I' and resid 133 through 134 removed outlier: 8.213A pdb=" N CYS I 134 " --> pdb=" O TYR I 78 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS I 80 " --> pdb=" O CYS I 134 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL I 147 " --> pdb=" O THR I 60 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN I 151 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL I 280 " --> pdb=" O VAL I 287 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N AARG I 289 " --> pdb=" O THR I 278 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N THR I 278 " --> pdb=" O AARG I 289 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR I 291 " --> pdb=" O CYS I 276 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N CYS I 276 " --> pdb=" O THR I 291 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N SER I 293 " --> pdb=" O CYS I 274 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N CYS I 274 " --> pdb=" O SER I 293 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 246 through 251 removed outlier: 3.638A pdb=" N THR I 197 " --> pdb=" O TYR I 192 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA I 189 " --> pdb=" O CYS I 331 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N TYR I 333 " --> pdb=" O ALA I 189 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ALA I 191 " --> pdb=" O TYR I 333 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 303 through 307 Processing sheet with id=AE1, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AE2, first strand: chain 'J' and resid 133 through 134 removed outlier: 8.213A pdb=" N CYS J 134 " --> pdb=" O TYR J 78 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS J 80 " --> pdb=" O CYS J 134 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL J 147 " --> pdb=" O THR J 60 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN J 151 " --> pdb=" O ILE J 64 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL J 280 " --> pdb=" O VAL J 287 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N AARG J 289 " --> pdb=" O THR J 278 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N THR J 278 " --> pdb=" O AARG J 289 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR J 291 " --> pdb=" O CYS J 276 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N CYS J 276 " --> pdb=" O THR J 291 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER J 293 " --> pdb=" O CYS J 274 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N CYS J 274 " --> pdb=" O SER J 293 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 246 through 251 removed outlier: 3.638A pdb=" N THR J 197 " --> pdb=" O TYR J 192 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ALA J 189 " --> pdb=" O CYS J 331 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N TYR J 333 " --> pdb=" O ALA J 189 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ALA J 191 " --> pdb=" O TYR J 333 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 303 through 307 Processing sheet with id=AE5, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'K' and resid 133 through 134 removed outlier: 8.212A pdb=" N CYS K 134 " --> pdb=" O TYR K 78 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS K 80 " --> pdb=" O CYS K 134 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL K 147 " --> pdb=" O THR K 60 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLN K 151 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL K 280 " --> pdb=" O VAL K 287 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N AARG K 289 " --> pdb=" O THR K 278 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N THR K 278 " --> pdb=" O AARG K 289 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N THR K 291 " --> pdb=" O CYS K 276 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N CYS K 276 " --> pdb=" O THR K 291 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N SER K 293 " --> pdb=" O CYS K 274 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N CYS K 274 " --> pdb=" O SER K 293 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 246 through 251 removed outlier: 3.638A pdb=" N THR K 197 " --> pdb=" O TYR K 192 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ALA K 189 " --> pdb=" O CYS K 331 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N TYR K 333 " --> pdb=" O ALA K 189 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ALA K 191 " --> pdb=" O TYR K 333 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 303 through 307 Processing sheet with id=AE9, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain 'L' and resid 133 through 134 removed outlier: 8.212A pdb=" N CYS L 134 " --> pdb=" O TYR L 78 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N CYS L 80 " --> pdb=" O CYS L 134 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL L 147 " --> pdb=" O THR L 60 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN L 151 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL L 280 " --> pdb=" O VAL L 287 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N AARG L 289 " --> pdb=" O THR L 278 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N THR L 278 " --> pdb=" O AARG L 289 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR L 291 " --> pdb=" O CYS L 276 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N CYS L 276 " --> pdb=" O THR L 291 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER L 293 " --> pdb=" O CYS L 274 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N CYS L 274 " --> pdb=" O SER L 293 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 246 through 251 removed outlier: 3.638A pdb=" N THR L 197 " --> pdb=" O TYR L 192 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ALA L 189 " --> pdb=" O CYS L 331 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N TYR L 333 " --> pdb=" O ALA L 189 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ALA L 191 " --> pdb=" O TYR L 333 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 303 through 307 1884 hydrogen bonds defined for protein. 5412 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: 10.95 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8203 1.33 - 1.45: 10900 1.45 - 1.58: 24637 1.58 - 1.70: 60 1.70 - 1.83: 528 Bond restraints: 44328 Sorted by residual: bond pdb=" O3B MGP E1003 " pdb=" PC MGP E1003 " ideal model delta sigma weight residual 1.745 1.598 0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" O3B MGP D1003 " pdb=" PC MGP D1003 " ideal model delta sigma weight residual 1.745 1.599 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" O3B MGP L1003 " pdb=" PC MGP L1003 " ideal model delta sigma weight residual 1.745 1.599 0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" O3B MGP J1003 " pdb=" PC MGP J1003 " ideal model delta sigma weight residual 1.745 1.599 0.146 2.00e-02 2.50e+03 5.31e+01 bond pdb=" O3B MGP B1003 " pdb=" PC MGP B1003 " ideal model delta sigma weight residual 1.745 1.599 0.146 2.00e-02 2.50e+03 5.30e+01 ... (remaining 44323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 57800 2.13 - 4.27: 1841 4.27 - 6.40: 359 6.40 - 8.53: 74 8.53 - 10.67: 118 Bond angle restraints: 60192 Sorted by residual: angle pdb=" C PRO H 83 " pdb=" N MET H 84 " pdb=" CA MET H 84 " ideal model delta sigma weight residual 123.33 114.08 9.25 1.64e+00 3.72e-01 3.18e+01 angle pdb=" C PRO F 83 " pdb=" N MET F 84 " pdb=" CA MET F 84 " ideal model delta sigma weight residual 123.33 114.11 9.22 1.64e+00 3.72e-01 3.16e+01 angle pdb=" C PRO E 83 " pdb=" N MET E 84 " pdb=" CA MET E 84 " ideal model delta sigma weight residual 123.33 114.13 9.20 1.64e+00 3.72e-01 3.15e+01 angle pdb=" C PRO K 83 " pdb=" N MET K 84 " pdb=" CA MET K 84 " ideal model delta sigma weight residual 123.33 114.14 9.19 1.64e+00 3.72e-01 3.14e+01 angle pdb=" C PRO C 83 " pdb=" N MET C 84 " pdb=" CA MET C 84 " ideal model delta sigma weight residual 123.33 114.15 9.18 1.64e+00 3.72e-01 3.13e+01 ... (remaining 60187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 23046 17.85 - 35.70: 2874 35.70 - 53.55: 780 53.55 - 71.40: 192 71.40 - 89.25: 72 Dihedral angle restraints: 26964 sinusoidal: 10992 harmonic: 15972 Sorted by residual: dihedral pdb=" CA SER H 66 " pdb=" C SER H 66 " pdb=" N ALA H 67 " pdb=" CA ALA H 67 " ideal model delta harmonic sigma weight residual 180.00 160.52 19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA SER L 66 " pdb=" C SER L 66 " pdb=" N ALA L 67 " pdb=" CA ALA L 67 " ideal model delta harmonic sigma weight residual 180.00 160.55 19.45 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA SER J 66 " pdb=" C SER J 66 " pdb=" N ALA J 67 " pdb=" CA ALA J 67 " ideal model delta harmonic sigma weight residual 180.00 160.56 19.44 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 26961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2826 0.030 - 0.060: 2033 0.060 - 0.091: 1116 0.091 - 0.121: 601 0.121 - 0.151: 156 Chirality restraints: 6732 Sorted by residual: chirality pdb=" CA PRO F 193 " pdb=" N PRO F 193 " pdb=" C PRO F 193 " pdb=" CB PRO F 193 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CA PRO J 193 " pdb=" N PRO J 193 " pdb=" C PRO J 193 " pdb=" CB PRO J 193 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CA PRO E 193 " pdb=" N PRO E 193 " pdb=" C PRO E 193 " pdb=" CB PRO E 193 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 6729 not shown) Planarity restraints: 7560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL I 125 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO I 126 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO I 126 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO I 126 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 125 " -0.048 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO F 126 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO F 126 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 126 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 125 " 0.048 5.00e-02 4.00e+02 7.29e-02 8.49e+00 pdb=" N PRO J 126 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO J 126 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO J 126 " 0.040 5.00e-02 4.00e+02 ... (remaining 7557 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 284 2.58 - 3.16: 34118 3.16 - 3.74: 68450 3.74 - 4.32: 101790 4.32 - 4.90: 159251 Nonbonded interactions: 363893 Sorted by model distance: nonbonded pdb="MG MG I1004 " pdb=" O HOH I1110 " model vdw 2.005 2.170 nonbonded pdb="MG MG A1004 " pdb=" O HOH A1110 " model vdw 2.005 2.170 nonbonded pdb="MG MG D1004 " pdb=" O HOH D1110 " model vdw 2.005 2.170 nonbonded pdb="MG MG C1004 " pdb=" O HOH C1110 " model vdw 2.006 2.170 nonbonded pdb="MG MG H1004 " pdb=" O HOH H1110 " model vdw 2.006 2.170 ... (remaining 363888 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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=0.50 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: 0.010 Normalize map: mean=0, sd=1: 10.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 0.820 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 45.190 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 : 0.007 0.147 44364 Z= 0.374 Angle : 1.030 10.669 60192 Z= 0.533 Chirality : 0.055 0.151 6732 Planarity : 0.006 0.073 7560 Dihedral : 17.701 89.252 16620 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.08 % Allowed : 18.96 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.11), residues: 5388 helix: 1.68 (0.13), residues: 1644 sheet: 0.64 (0.15), residues: 1080 loop : -1.61 (0.11), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 229 TYR 0.014 0.002 TYR G 192 PHE 0.028 0.002 PHE I 183 TRP 0.011 0.002 TRP G 175 HIS 0.008 0.002 HIS F 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.37 (44328) covalent geometry : angle 1.03007 / 0.53 (60192) hydrogen bonds : bond 0.18314 / 12.38 ( 1884) hydrogen bonds : angle 6.22644 / 4.30 ( 5412) metal coordination : bond 0.00653 / 0.42 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 428 time to evaluate : 1.648 Fit side-chains REVERT: C 314 MET cc_start: 0.7794 (ttt) cc_final: 0.7537 (ttt) REVERT: F 84 MET cc_start: 0.6710 (mmm) cc_final: 0.6497 (mmm) REVERT: F 314 MET cc_start: 0.7659 (ttt) cc_final: 0.7339 (ttt) REVERT: I 314 MET cc_start: 0.7680 (ttt) cc_final: 0.7465 (ttt) REVERT: L 84 MET cc_start: 0.6478 (mmm) cc_final: 0.6246 (mmm) outliers start: 96 outliers final: 77 residues processed: 511 average time/residue: 0.7436 time to fit residues: 465.9906 Evaluate side-chains 466 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 389 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 427 LYS Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 414 THR Chi-restraints excluded: chain E residue 427 LYS Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 414 THR Chi-restraints excluded: chain G residue 427 LYS Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 427 LYS Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 414 THR Chi-restraints excluded: chain J residue 427 LYS Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain K residue 414 THR Chi-restraints excluded: chain K residue 427 LYS Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 59 SER Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 113 SER Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 414 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 394 optimal weight: 8.9990 chunk 430 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 8.9990 chunk 523 optimal weight: 10.0000 chunk 497 optimal weight: 0.1980 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 0.6980 chunk 488 optimal weight: 0.9980 chunk 366 optimal weight: 0.9980 chunk 223 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 95 ASN C 95 ASN D 95 ASN E 95 ASN F 95 ASN G 95 ASN H 95 ASN I 95 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.145480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.107447 restraints weight = 146013.104| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.50 r_work: 0.3062 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 44364 Z= 0.149 Angle : 0.599 5.372 60192 Z= 0.327 Chirality : 0.044 0.133 6732 Planarity : 0.005 0.058 7560 Dihedral : 7.499 55.266 6558 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.08 % Allowed : 17.88 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.11), residues: 5388 helix: 3.03 (0.13), residues: 1644 sheet: 1.03 (0.14), residues: 1140 loop : -1.59 (0.11), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 221 TYR 0.012 0.001 TYR E 150 PHE 0.016 0.001 PHE B 183 TRP 0.006 0.001 TRP J 470 HIS 0.004 0.001 HIS L 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (44328) covalent geometry : angle 0.59947 / 0.33 (60192) hydrogen bonds : bond 0.05721 / 3.91 ( 1884) hydrogen bonds : angle 4.72632 / 3.25 ( 5412) metal coordination : bond 0.00435 / 0.29 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 397 time to evaluate : 1.541 Fit side-chains REVERT: A 285 TYR cc_start: 0.9086 (OUTLIER) cc_final: 0.8050 (t80) REVERT: B 28 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: B 91 GLU cc_start: 0.7720 (tp30) cc_final: 0.7499 (mp0) REVERT: B 285 TYR cc_start: 0.9151 (OUTLIER) cc_final: 0.8550 (t80) REVERT: B 470 TRP cc_start: 0.7290 (t60) cc_final: 0.7018 (t60) REVERT: D 232 LYS cc_start: 0.7638 (pptt) cc_final: 0.7394 (ttpt) REVERT: D 285 TYR cc_start: 0.9082 (OUTLIER) cc_final: 0.8019 (t80) REVERT: E 16 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7932 (tmmt) REVERT: E 28 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: E 285 TYR cc_start: 0.9145 (OUTLIER) cc_final: 0.8603 (t80) REVERT: G 16 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7821 (tmmt) REVERT: G 232 LYS cc_start: 0.7701 (pptt) cc_final: 0.7451 (ttpt) REVERT: G 285 TYR cc_start: 0.9078 (OUTLIER) cc_final: 0.8125 (t80) REVERT: G 470 TRP cc_start: 0.7035 (t60) cc_final: 0.6734 (t60) REVERT: H 16 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7945 (tmmt) REVERT: H 28 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: H 285 TYR cc_start: 0.9141 (OUTLIER) cc_final: 0.8523 (t80) REVERT: J 16 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7852 (tmmt) REVERT: J 232 LYS cc_start: 0.7572 (pptt) cc_final: 0.7370 (ttpt) REVERT: J 285 TYR cc_start: 0.9086 (OUTLIER) cc_final: 0.8040 (t80) REVERT: K 28 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: K 285 TYR cc_start: 0.9148 (OUTLIER) cc_final: 0.8551 (t80) REVERT: K 470 TRP cc_start: 0.7285 (t60) cc_final: 0.7026 (t60) outliers start: 96 outliers final: 32 residues processed: 464 average time/residue: 0.7667 time to fit residues: 434.2558 Evaluate side-chains 401 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 353 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain J residue 16 LYS Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 410 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 102 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 403 optimal weight: 10.0000 chunk 473 optimal weight: 4.9990 chunk 308 optimal weight: 3.9990 chunk 182 optimal weight: 0.3980 chunk 345 optimal weight: 10.0000 chunk 163 optimal weight: 0.6980 chunk 261 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN B 95 ASN C 95 ASN D 95 ASN E 95 ASN F 95 ASN G 95 ASN I 95 ASN J 95 ASN K 95 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.142220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.103811 restraints weight = 145554.969| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.42 r_work: 0.3007 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 44364 Z= 0.183 Angle : 0.642 5.163 60192 Z= 0.352 Chirality : 0.045 0.136 6732 Planarity : 0.005 0.052 7560 Dihedral : 7.279 53.771 6468 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.45 % Allowed : 17.97 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.11), residues: 5388 helix: 3.10 (0.13), residues: 1644 sheet: 1.16 (0.15), residues: 1020 loop : -1.60 (0.10), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.015 0.002 TYR K 150 PHE 0.018 0.002 PHE C 183 TRP 0.010 0.001 TRP L 175 HIS 0.006 0.001 HIS L 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.18 (44328) covalent geometry : angle 0.64213 / 0.35 (60192) hydrogen bonds : bond 0.07473 / 5.10 ( 1884) hydrogen bonds : angle 4.82075 / 3.32 ( 5412) metal coordination : bond 0.00516 / 0.33 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 372 time to evaluate : 1.656 Fit side-chains REVERT: A 285 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.7820 (t80) REVERT: A 441 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8602 (mp10) REVERT: B 28 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: B 84 MET cc_start: 0.7289 (mmm) cc_final: 0.6854 (mmm) REVERT: B 208 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8356 (tttm) REVERT: B 285 TYR cc_start: 0.9219 (OUTLIER) cc_final: 0.8477 (t80) REVERT: B 292 MET cc_start: 0.8792 (mtm) cc_final: 0.8521 (mtm) REVERT: C 28 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: C 208 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8387 (tttm) REVERT: D 28 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: D 285 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.7825 (t80) REVERT: E 16 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7921 (tmmt) REVERT: E 28 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: E 208 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8370 (tttm) REVERT: E 285 TYR cc_start: 0.9215 (OUTLIER) cc_final: 0.8464 (t80) REVERT: E 292 MET cc_start: 0.8813 (mtm) cc_final: 0.8544 (mtm) REVERT: F 28 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: F 208 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8389 (tttm) REVERT: G 16 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7854 (tmmt) REVERT: G 28 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: G 232 LYS cc_start: 0.7649 (pptt) cc_final: 0.7439 (ttpt) REVERT: G 285 TYR cc_start: 0.9122 (OUTLIER) cc_final: 0.7824 (t80) REVERT: H 16 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7912 (tmmt) REVERT: H 28 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: H 208 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8359 (tttm) REVERT: H 285 TYR cc_start: 0.9214 (OUTLIER) cc_final: 0.8462 (t80) REVERT: H 292 MET cc_start: 0.8819 (mtm) cc_final: 0.8552 (mtm) REVERT: I 28 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: J 232 LYS cc_start: 0.7598 (pptt) cc_final: 0.7364 (ttpt) REVERT: J 285 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.7818 (t80) REVERT: K 28 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: K 91 GLU cc_start: 0.7792 (tp30) cc_final: 0.7554 (mp0) REVERT: K 208 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8349 (tttm) REVERT: K 285 TYR cc_start: 0.9215 (OUTLIER) cc_final: 0.8473 (t80) REVERT: K 292 MET cc_start: 0.8799 (mtm) cc_final: 0.8522 (mtm) REVERT: L 28 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: L 208 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8389 (tttm) outliers start: 113 outliers final: 48 residues processed: 479 average time/residue: 0.7611 time to fit residues: 443.6122 Evaluate side-chains 437 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 360 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 208 LYS Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 208 LYS Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 113 SER Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 414 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 95 optimal weight: 5.9990 chunk 276 optimal weight: 9.9990 chunk 330 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 322 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 293 optimal weight: 0.2980 chunk 130 optimal weight: 8.9990 chunk 411 optimal weight: 9.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN A 157 HIS B 95 ASN B 157 HIS C 95 ASN D 95 ASN D 157 HIS E 95 ASN E 157 HIS F 95 ASN G 95 ASN G 157 HIS H 157 HIS I 95 ASN J 95 ASN J 157 HIS K 95 ASN K 157 HIS L 95 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.139982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.101061 restraints weight = 161321.934| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.58 r_work: 0.2954 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 44364 Z= 0.251 Angle : 0.764 6.692 60192 Z= 0.421 Chirality : 0.049 0.140 6732 Planarity : 0.005 0.051 7560 Dihedral : 7.569 52.948 6468 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.66 % Allowed : 18.03 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.11), residues: 5388 helix: 2.79 (0.12), residues: 1656 sheet: 0.92 (0.15), residues: 1032 loop : -1.56 (0.10), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 221 TYR 0.017 0.002 TYR K 150 PHE 0.028 0.002 PHE C 183 TRP 0.009 0.002 TRP I 175 HIS 0.007 0.002 HIS E 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.25 (44328) covalent geometry : angle 0.76374 / 0.42 (60192) hydrogen bonds : bond 0.09285 / 6.31 ( 1884) hydrogen bonds : angle 5.08519 / 3.51 ( 5412) metal coordination : bond 0.00796 / 0.52 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 378 time to evaluate : 1.323 Fit side-chains REVERT: A 16 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7854 (tmmt) REVERT: A 208 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8652 (tttm) REVERT: A 285 TYR cc_start: 0.9175 (OUTLIER) cc_final: 0.7869 (t80) REVERT: A 389 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8666 (tp-100) REVERT: B 28 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: B 84 MET cc_start: 0.7478 (mmm) cc_final: 0.7085 (mmm) REVERT: B 208 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8399 (tttm) REVERT: B 285 TYR cc_start: 0.9242 (OUTLIER) cc_final: 0.8525 (t80) REVERT: B 292 MET cc_start: 0.8865 (mtm) cc_final: 0.8530 (mtm) REVERT: B 446 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8044 (mt-10) REVERT: C 28 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: C 446 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8381 (mp0) REVERT: D 28 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: D 285 TYR cc_start: 0.9179 (OUTLIER) cc_final: 0.7876 (t80) REVERT: E 16 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8006 (tmmt) REVERT: E 28 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: E 208 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8412 (tttm) REVERT: E 285 TYR cc_start: 0.9242 (OUTLIER) cc_final: 0.8527 (t80) REVERT: E 292 MET cc_start: 0.8872 (mtm) cc_final: 0.8530 (mtm) REVERT: E 446 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8062 (mt-10) REVERT: F 28 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: G 16 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7881 (tmmt) REVERT: G 28 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: G 285 TYR cc_start: 0.9177 (OUTLIER) cc_final: 0.7876 (t80) REVERT: H 16 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8009 (tmmt) REVERT: H 28 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: H 208 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8404 (tttm) REVERT: H 285 TYR cc_start: 0.9239 (OUTLIER) cc_final: 0.8523 (t80) REVERT: H 292 MET cc_start: 0.8870 (mtm) cc_final: 0.8527 (mtm) REVERT: H 446 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8070 (mt-10) REVERT: I 28 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: J 16 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7864 (tmmt) REVERT: J 285 TYR cc_start: 0.9173 (OUTLIER) cc_final: 0.7863 (t80) REVERT: K 28 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: K 208 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8398 (tttm) REVERT: K 285 TYR cc_start: 0.9242 (OUTLIER) cc_final: 0.8527 (t80) REVERT: K 292 MET cc_start: 0.8865 (mtm) cc_final: 0.8522 (mtm) REVERT: K 446 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: L 28 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: L 446 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8403 (mp0) outliers start: 123 outliers final: 61 residues processed: 487 average time/residue: 0.7428 time to fit residues: 441.4220 Evaluate side-chains 467 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 371 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 414 THR Chi-restraints excluded: chain G residue 446 GLU Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 446 GLU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain J residue 16 LYS Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 414 THR Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 208 LYS Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain K residue 446 GLU Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 113 SER Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain L residue 446 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 514 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 347 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 509 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN B 95 ASN C 95 ASN D 95 ASN E 95 ASN F 95 ASN G 95 ASN I 95 ASN J 95 ASN K 95 ASN L 95 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.139291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.100415 restraints weight = 144979.208| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.49 r_work: 0.2947 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 44364 Z= 0.264 Angle : 0.793 7.413 60192 Z= 0.436 Chirality : 0.050 0.141 6732 Planarity : 0.006 0.054 7560 Dihedral : 7.623 52.815 6468 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.03 % Allowed : 18.12 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.11), residues: 5388 helix: 2.63 (0.12), residues: 1656 sheet: 0.97 (0.15), residues: 972 loop : -1.55 (0.10), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 221 TYR 0.018 0.002 TYR B 150 PHE 0.030 0.003 PHE F 183 TRP 0.009 0.002 TRP C 175 HIS 0.008 0.002 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.26 (44328) covalent geometry : angle 0.79305 / 0.44 (60192) hydrogen bonds : bond 0.09531 / 6.47 ( 1884) hydrogen bonds : angle 5.11705 / 3.53 ( 5412) metal coordination : bond 0.00882 / 0.57 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 381 time to evaluate : 1.751 Fit side-chains REVERT: A 16 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7889 (tmmt) REVERT: A 28 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: A 285 TYR cc_start: 0.9189 (OUTLIER) cc_final: 0.7889 (t80) REVERT: A 389 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8692 (tp-100) REVERT: A 441 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8529 (mp10) REVERT: B 28 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: B 208 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8428 (tttm) REVERT: B 285 TYR cc_start: 0.9237 (OUTLIER) cc_final: 0.8531 (t80) REVERT: B 446 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: C 28 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: C 441 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8459 (mp10) REVERT: C 446 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: D 28 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: D 285 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.7895 (t80) REVERT: D 441 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8530 (mp10) REVERT: E 16 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8041 (tmmt) REVERT: E 28 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: E 208 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8432 (tttm) REVERT: E 285 TYR cc_start: 0.9235 (OUTLIER) cc_final: 0.8528 (t80) REVERT: E 446 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: F 28 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: F 441 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8459 (mp10) REVERT: F 446 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8279 (mp0) REVERT: G 16 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7904 (tmmt) REVERT: G 28 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: G 232 LYS cc_start: 0.7719 (pptt) cc_final: 0.7507 (ttpt) REVERT: G 285 TYR cc_start: 0.9189 (OUTLIER) cc_final: 0.7891 (t80) REVERT: G 441 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8525 (mp10) REVERT: H 16 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8033 (tmmt) REVERT: H 28 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: H 208 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8429 (tttm) REVERT: H 285 TYR cc_start: 0.9231 (OUTLIER) cc_final: 0.8522 (t80) REVERT: H 446 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8088 (mt-10) REVERT: I 28 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: I 208 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8408 (tttt) REVERT: I 441 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8457 (mp10) REVERT: I 446 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8292 (mp0) REVERT: J 16 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7892 (tmmt) REVERT: J 28 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: J 285 TYR cc_start: 0.9184 (OUTLIER) cc_final: 0.7878 (t80) REVERT: J 441 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8528 (mp10) REVERT: K 28 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: K 208 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8424 (tttm) REVERT: K 285 TYR cc_start: 0.9238 (OUTLIER) cc_final: 0.8534 (t80) REVERT: K 446 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: L 28 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: L 446 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8395 (mp0) outliers start: 140 outliers final: 69 residues processed: 506 average time/residue: 0.7295 time to fit residues: 452.3785 Evaluate side-chains 491 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 376 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain F residue 446 GLU Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 414 THR Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain G residue 446 GLU Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 446 GLU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 208 LYS Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 441 GLN Chi-restraints excluded: chain I residue 446 GLU Chi-restraints excluded: chain J residue 16 LYS Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 414 THR Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 208 LYS Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain K residue 446 GLU Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 113 SER Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain L residue 446 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 374 optimal weight: 10.0000 chunk 462 optimal weight: 9.9990 chunk 375 optimal weight: 8.9990 chunk 274 optimal weight: 4.9990 chunk 520 optimal weight: 8.9990 chunk 234 optimal weight: 0.8980 chunk 323 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 499 optimal weight: 4.9990 chunk 216 optimal weight: 0.1980 chunk 242 optimal weight: 2.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN B 95 ASN C 95 ASN D 95 ASN E 95 ASN F 95 ASN G 95 ASN I 95 ASN J 95 ASN K 95 ASN L 95 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.140286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.101756 restraints weight = 150270.024| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.50 r_work: 0.2963 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 44364 Z= 0.239 Angle : 0.743 6.413 60192 Z= 0.410 Chirality : 0.049 0.137 6732 Planarity : 0.005 0.054 7560 Dihedral : 7.569 53.065 6468 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.79 % Allowed : 18.42 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.11), residues: 5388 helix: 2.75 (0.12), residues: 1656 sheet: 0.89 (0.15), residues: 1032 loop : -1.57 (0.10), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 221 TYR 0.017 0.002 TYR B 150 PHE 0.027 0.002 PHE L 183 TRP 0.009 0.002 TRP F 175 HIS 0.006 0.002 HIS G 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.24 (44328) covalent geometry : angle 0.74337 / 0.41 (60192) hydrogen bonds : bond 0.08872 / 6.03 ( 1884) hydrogen bonds : angle 5.04388 / 3.48 ( 5412) metal coordination : bond 0.00784 / 0.50 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 376 time to evaluate : 1.824 Fit side-chains REVERT: A 16 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7858 (tmmt) REVERT: A 28 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: A 285 TYR cc_start: 0.9169 (OUTLIER) cc_final: 0.7968 (t80) REVERT: A 389 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8660 (tp-100) REVERT: B 28 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: B 208 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8400 (tttm) REVERT: B 285 TYR cc_start: 0.9234 (OUTLIER) cc_final: 0.8521 (t80) REVERT: B 292 MET cc_start: 0.8864 (mtm) cc_final: 0.8531 (mtm) REVERT: B 446 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8005 (mt-10) REVERT: C 28 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: C 208 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8403 (tttm) REVERT: C 441 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8429 (mp10) REVERT: C 446 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: D 28 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: D 285 TYR cc_start: 0.9174 (OUTLIER) cc_final: 0.7979 (t80) REVERT: E 16 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.7965 (tmmt) REVERT: E 28 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: E 208 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8404 (tttm) REVERT: E 285 TYR cc_start: 0.9233 (OUTLIER) cc_final: 0.8519 (t80) REVERT: E 292 MET cc_start: 0.8870 (mtm) cc_final: 0.8529 (mtm) REVERT: E 446 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8029 (mt-10) REVERT: F 28 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: F 208 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8406 (tttm) REVERT: F 441 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8427 (mp10) REVERT: G 16 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7873 (tmmt) REVERT: G 28 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: G 285 TYR cc_start: 0.9170 (OUTLIER) cc_final: 0.7973 (t80) REVERT: H 16 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.7961 (tmmt) REVERT: H 28 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: H 208 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8401 (tttm) REVERT: H 285 TYR cc_start: 0.9229 (OUTLIER) cc_final: 0.8516 (t80) REVERT: H 292 MET cc_start: 0.8866 (mtm) cc_final: 0.8525 (mtm) REVERT: H 446 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8051 (mt-10) REVERT: I 28 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: I 208 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8381 (tttt) REVERT: I 441 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8430 (mp10) REVERT: J 16 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7859 (tmmt) REVERT: J 28 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: J 285 TYR cc_start: 0.9167 (OUTLIER) cc_final: 0.7962 (t80) REVERT: K 28 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: K 208 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8396 (tttm) REVERT: K 285 TYR cc_start: 0.9232 (OUTLIER) cc_final: 0.8521 (t80) REVERT: K 292 MET cc_start: 0.8866 (mtm) cc_final: 0.8528 (mtm) REVERT: K 446 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: L 28 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: L 208 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8407 (tttm) REVERT: L 446 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8392 (mp0) outliers start: 129 outliers final: 68 residues processed: 486 average time/residue: 0.6847 time to fit residues: 409.2496 Evaluate side-chains 482 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 371 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 208 LYS Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 414 THR Chi-restraints excluded: chain G residue 446 GLU Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 446 GLU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 208 LYS Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 441 GLN Chi-restraints excluded: chain J residue 16 LYS Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 414 THR Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 208 LYS Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain K residue 446 GLU Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 113 SER Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain L residue 446 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 403 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 chunk 198 optimal weight: 0.5980 chunk 505 optimal weight: 9.9990 chunk 477 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 205 optimal weight: 20.0000 chunk 385 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN B 95 ASN C 95 ASN D 95 ASN E 95 ASN F 95 ASN G 95 ASN I 95 ASN I 157 HIS J 95 ASN K 95 ASN L 95 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.142604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.104180 restraints weight = 155891.171| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.53 r_work: 0.3009 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 44364 Z= 0.173 Angle : 0.630 5.888 60192 Z= 0.345 Chirality : 0.045 0.133 6732 Planarity : 0.005 0.053 7560 Dihedral : 7.237 53.528 6468 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.90 % Allowed : 18.40 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.11), residues: 5388 helix: 3.11 (0.13), residues: 1644 sheet: 1.03 (0.15), residues: 1032 loop : -1.55 (0.10), residues: 2712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 221 TYR 0.014 0.001 TYR K 150 PHE 0.018 0.002 PHE C 183 TRP 0.008 0.001 TRP C 175 HIS 0.005 0.001 HIS L 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 (44328) covalent geometry : angle 0.63018 / 0.34 (60192) hydrogen bonds : bond 0.06933 / 4.73 ( 1884) hydrogen bonds : angle 4.77158 / 3.29 ( 5412) metal coordination : bond 0.00506 / 0.33 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 369 time to evaluate : 1.353 Fit side-chains REVERT: A 16 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7879 (tmmt) REVERT: A 28 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: A 285 TYR cc_start: 0.9131 (OUTLIER) cc_final: 0.7963 (t80) REVERT: B 28 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: B 208 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8397 (tttm) REVERT: B 285 TYR cc_start: 0.9212 (OUTLIER) cc_final: 0.8561 (t80) REVERT: B 292 MET cc_start: 0.8805 (mtm) cc_final: 0.8555 (mtm) REVERT: B 446 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: C 28 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: C 208 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8397 (tttm) REVERT: C 232 LYS cc_start: 0.7690 (ttpt) cc_final: 0.7432 (tttt) REVERT: C 441 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8375 (mp10) REVERT: D 28 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: D 285 TYR cc_start: 0.9143 (OUTLIER) cc_final: 0.7989 (t80) REVERT: E 16 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.7969 (tmmt) REVERT: E 28 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: E 208 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8399 (tttm) REVERT: E 285 TYR cc_start: 0.9210 (OUTLIER) cc_final: 0.8557 (t80) REVERT: E 292 MET cc_start: 0.8814 (mtm) cc_final: 0.8561 (mtm) REVERT: E 446 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: F 208 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8391 (tttm) REVERT: F 441 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8373 (mp10) REVERT: F 446 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8289 (mp0) REVERT: G 16 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7884 (tmmt) REVERT: G 28 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: G 285 TYR cc_start: 0.9133 (OUTLIER) cc_final: 0.7968 (t80) REVERT: H 16 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.7960 (tmmt) REVERT: H 28 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: H 208 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8392 (tttm) REVERT: H 285 TYR cc_start: 0.9207 (OUTLIER) cc_final: 0.8551 (t80) REVERT: H 292 MET cc_start: 0.8814 (mtm) cc_final: 0.8561 (mtm) REVERT: H 446 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: I 28 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: I 441 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8370 (mp10) REVERT: I 446 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8302 (mp0) REVERT: J 16 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7878 (tmmt) REVERT: J 28 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: J 285 TYR cc_start: 0.9132 (OUTLIER) cc_final: 0.7960 (t80) REVERT: K 28 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: K 208 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8391 (tttm) REVERT: K 285 TYR cc_start: 0.9211 (OUTLIER) cc_final: 0.8560 (t80) REVERT: K 292 MET cc_start: 0.8807 (mtm) cc_final: 0.8556 (mtm) REVERT: K 446 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: L 28 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: L 208 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8383 (tttm) REVERT: L 441 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8399 (mp10) outliers start: 134 outliers final: 63 residues processed: 492 average time/residue: 0.6248 time to fit residues: 376.9188 Evaluate side-chains 469 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 365 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 208 LYS Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain F residue 446 GLU Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 414 THR Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 446 GLU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 410 VAL Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 441 GLN Chi-restraints excluded: chain I residue 446 GLU Chi-restraints excluded: chain J residue 16 LYS Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 410 VAL Chi-restraints excluded: chain J residue 414 THR Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 75 ASP Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 208 LYS Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 446 GLU Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 113 SER Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 410 VAL Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain L residue 441 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 85 optimal weight: 10.0000 chunk 376 optimal weight: 10.0000 chunk 242 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 294 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 64 optimal weight: 0.0270 chunk 200 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 111 optimal weight: 0.0000 overall best weight: 1.3446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN B 95 ASN C 95 ASN D 95 ASN E 95 ASN F 95 ASN G 95 ASN I 95 ASN J 95 ASN K 95 ASN L 95 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.143031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.104623 restraints weight = 146588.436| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.51 r_work: 0.3016 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 44364 Z= 0.165 Angle : 0.613 6.412 60192 Z= 0.334 Chirality : 0.044 0.132 6732 Planarity : 0.005 0.053 7560 Dihedral : 7.028 53.507 6466 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.38 % Allowed : 18.94 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.11), residues: 5388 helix: 3.25 (0.13), residues: 1644 sheet: 0.97 (0.14), residues: 1152 loop : -1.46 (0.11), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 221 TYR 0.013 0.001 TYR B 150 PHE 0.017 0.002 PHE C 183 TRP 0.008 0.001 TRP F 175 HIS 0.005 0.001 HIS F 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.17 (44328) covalent geometry : angle 0.61312 / 0.33 (60192) hydrogen bonds : bond 0.06605 / 4.51 ( 1884) hydrogen bonds : angle 4.66272 / 3.22 ( 5412) metal coordination : bond 0.00476 / 0.31 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 361 time to evaluate : 1.207 Fit side-chains REVERT: A 16 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7886 (tmmt) REVERT: A 28 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: A 285 TYR cc_start: 0.9127 (OUTLIER) cc_final: 0.7931 (t80) REVERT: B 28 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: B 208 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8388 (tttm) REVERT: B 285 TYR cc_start: 0.9208 (OUTLIER) cc_final: 0.8530 (t80) REVERT: B 292 MET cc_start: 0.8798 (mtm) cc_final: 0.8539 (mtm) REVERT: B 446 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: C 28 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: C 208 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8380 (tttm) REVERT: C 232 LYS cc_start: 0.7757 (ttpt) cc_final: 0.7551 (tmmm) REVERT: C 441 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8438 (mp10) REVERT: D 28 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: D 285 TYR cc_start: 0.9135 (OUTLIER) cc_final: 0.7952 (t80) REVERT: E 16 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7988 (tmmt) REVERT: E 28 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: E 208 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8390 (tttm) REVERT: E 285 TYR cc_start: 0.9206 (OUTLIER) cc_final: 0.8528 (t80) REVERT: E 292 MET cc_start: 0.8801 (mtm) cc_final: 0.8537 (mtm) REVERT: E 446 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7952 (mt-10) REVERT: F 28 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: F 208 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8380 (tttm) REVERT: F 441 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8432 (mp10) REVERT: F 446 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8297 (mp0) REVERT: G 16 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7889 (tmmt) REVERT: G 28 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: G 285 TYR cc_start: 0.9127 (OUTLIER) cc_final: 0.7937 (t80) REVERT: H 16 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7969 (tmmt) REVERT: H 28 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: H 208 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8378 (tttm) REVERT: H 285 TYR cc_start: 0.9202 (OUTLIER) cc_final: 0.8521 (t80) REVERT: H 292 MET cc_start: 0.8806 (mtm) cc_final: 0.8544 (mtm) REVERT: H 446 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7962 (mt-10) REVERT: I 28 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: I 441 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8434 (mp10) REVERT: I 446 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8306 (mp0) REVERT: J 16 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7891 (tmmt) REVERT: J 28 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: J 285 TYR cc_start: 0.9126 (OUTLIER) cc_final: 0.7933 (t80) REVERT: K 28 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: K 208 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8379 (tttm) REVERT: K 285 TYR cc_start: 0.9208 (OUTLIER) cc_final: 0.8532 (t80) REVERT: K 292 MET cc_start: 0.8799 (mtm) cc_final: 0.8539 (mtm) REVERT: K 446 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: L 28 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: L 208 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8385 (tttm) REVERT: L 441 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8386 (mp10) outliers start: 110 outliers final: 54 residues processed: 461 average time/residue: 0.6084 time to fit residues: 341.4507 Evaluate side-chains 453 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 357 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 208 LYS Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain F residue 446 GLU Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 228 MET Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 414 THR Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 446 GLU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 441 GLN Chi-restraints excluded: chain I residue 446 GLU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 16 LYS Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 414 THR Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 208 LYS Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 446 GLU Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 113 SER Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain L residue 441 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 182 optimal weight: 4.9990 chunk 341 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 516 optimal weight: 0.3980 chunk 81 optimal weight: 5.9990 chunk 425 optimal weight: 7.9990 chunk 427 optimal weight: 5.9990 chunk 245 optimal weight: 9.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN B 95 ASN C 95 ASN C 157 HIS D 95 ASN E 95 ASN F 95 ASN G 95 ASN I 95 ASN J 95 ASN K 95 ASN L 95 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.138676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.100218 restraints weight = 137214.744| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.40 r_work: 0.2939 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 44364 Z= 0.322 Angle : 0.883 8.517 60192 Z= 0.486 Chirality : 0.054 0.167 6732 Planarity : 0.006 0.053 7560 Dihedral : 7.573 53.196 6456 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.47 % Allowed : 18.70 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.11), residues: 5388 helix: 2.53 (0.12), residues: 1656 sheet: 0.91 (0.15), residues: 996 loop : -1.50 (0.10), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 221 TYR 0.020 0.003 TYR B 150 PHE 0.035 0.003 PHE C 183 TRP 0.010 0.002 TRP K 199 HIS 0.009 0.002 HIS J 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.32 (44328) covalent geometry : angle 0.88260 / 0.49 (60192) hydrogen bonds : bond 0.10694 / 7.25 ( 1884) hydrogen bonds : angle 5.22782 / 3.60 ( 5412) metal coordination : bond 0.01109 / 0.71 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 386 time to evaluate : 1.061 Fit side-chains REVERT: A 16 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7846 (tmmt) REVERT: A 28 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: A 285 TYR cc_start: 0.9199 (OUTLIER) cc_final: 0.7932 (t80) REVERT: A 389 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8686 (tp-100) REVERT: A 441 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8499 (mp10) REVERT: B 28 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: B 208 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8449 (tttm) REVERT: B 285 TYR cc_start: 0.9246 (OUTLIER) cc_final: 0.8458 (t80) REVERT: B 292 MET cc_start: 0.8881 (mtm) cc_final: 0.8474 (mtm) REVERT: B 446 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: C 28 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: D 28 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: D 285 TYR cc_start: 0.9204 (OUTLIER) cc_final: 0.7939 (t80) REVERT: D 441 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8501 (mp10) REVERT: E 16 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.7992 (tmmt) REVERT: E 28 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: E 208 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8454 (tttm) REVERT: E 285 TYR cc_start: 0.9245 (OUTLIER) cc_final: 0.8460 (t80) REVERT: E 292 MET cc_start: 0.8884 (mtm) cc_final: 0.8472 (mtm) REVERT: E 446 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: F 446 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8266 (mp0) REVERT: G 16 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7854 (tmmt) REVERT: G 28 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: G 285 TYR cc_start: 0.9199 (OUTLIER) cc_final: 0.7932 (t80) REVERT: G 441 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8497 (mp10) REVERT: H 16 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7988 (tmmt) REVERT: H 28 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: H 208 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8448 (tttm) REVERT: H 285 TYR cc_start: 0.9243 (OUTLIER) cc_final: 0.8458 (t80) REVERT: H 292 MET cc_start: 0.8880 (mtm) cc_final: 0.8467 (mtm) REVERT: H 446 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8075 (mt-10) REVERT: I 28 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: I 208 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8440 (tttt) REVERT: I 446 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8280 (mp0) REVERT: J 16 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7846 (tmmt) REVERT: J 28 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: J 285 TYR cc_start: 0.9197 (OUTLIER) cc_final: 0.7927 (t80) REVERT: J 441 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8494 (mp10) REVERT: K 28 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: K 208 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8444 (tttm) REVERT: K 285 TYR cc_start: 0.9245 (OUTLIER) cc_final: 0.8462 (t80) REVERT: K 292 MET cc_start: 0.8878 (mtm) cc_final: 0.8466 (mtm) REVERT: K 446 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: L 28 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: L 441 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8438 (mp10) outliers start: 114 outliers final: 56 residues processed: 485 average time/residue: 0.5109 time to fit residues: 304.5069 Evaluate side-chains 478 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 381 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 446 GLU Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 414 THR Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain H residue 446 GLU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 208 LYS Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 446 GLU Chi-restraints excluded: chain J residue 16 LYS Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 414 THR Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 208 LYS Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 446 GLU Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 113 SER Chi-restraints excluded: chain L residue 414 THR Chi-restraints excluded: chain L residue 441 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 463 optimal weight: 20.0000 chunk 316 optimal weight: 0.9990 chunk 529 optimal weight: 5.9990 chunk 131 optimal weight: 0.6980 chunk 325 optimal weight: 5.9990 chunk 402 optimal weight: 5.9990 chunk 323 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 475 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 147 optimal weight: 0.0010 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN B 95 ASN C 95 ASN D 95 ASN E 95 ASN F 95 ASN G 95 ASN I 95 ASN J 95 ASN K 95 ASN L 95 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.143512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.105060 restraints weight = 160546.756| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.68 r_work: 0.3022 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 44364 Z= 0.156 Angle : 0.603 6.800 60192 Z= 0.328 Chirality : 0.044 0.132 6732 Planarity : 0.005 0.053 7560 Dihedral : 7.060 52.974 6456 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.06 % Allowed : 19.44 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.11), residues: 5388 helix: 3.09 (0.13), residues: 1656 sheet: 0.96 (0.14), residues: 1152 loop : -1.48 (0.11), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 221 TYR 0.013 0.001 TYR K 150 PHE 0.015 0.001 PHE F 183 TRP 0.007 0.001 TRP I 175 HIS 0.004 0.001 HIS F 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.16 (44328) covalent geometry : angle 0.60309 / 0.33 (60192) hydrogen bonds : bond 0.06232 / 4.26 ( 1884) hydrogen bonds : angle 4.68333 / 3.23 ( 5412) metal coordination : bond 0.00427 / 0.28 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 373 time to evaluate : 1.068 Fit side-chains REVERT: A 28 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: A 285 TYR cc_start: 0.9123 (OUTLIER) cc_final: 0.7944 (t80) REVERT: A 389 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8494 (tp-100) REVERT: A 441 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8533 (mp10) REVERT: B 28 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: B 285 TYR cc_start: 0.9195 (OUTLIER) cc_final: 0.8601 (t80) REVERT: B 292 MET cc_start: 0.8814 (mtm) cc_final: 0.8563 (mtm) REVERT: C 28 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: C 208 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8417 (tttm) REVERT: D 28 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: D 285 TYR cc_start: 0.9125 (OUTLIER) cc_final: 0.7956 (t80) REVERT: D 441 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8536 (mp10) REVERT: E 16 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8013 (tmmt) REVERT: E 28 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: E 285 TYR cc_start: 0.9195 (OUTLIER) cc_final: 0.8602 (t80) REVERT: E 292 MET cc_start: 0.8817 (mtm) cc_final: 0.8566 (mtm) REVERT: E 446 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: F 208 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8416 (tttm) REVERT: F 446 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8284 (mp0) REVERT: G 285 TYR cc_start: 0.9123 (OUTLIER) cc_final: 0.7949 (t80) REVERT: G 441 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8528 (mp10) REVERT: H 16 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8001 (tmmt) REVERT: H 28 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: H 285 TYR cc_start: 0.9192 (OUTLIER) cc_final: 0.8596 (t80) REVERT: H 292 MET cc_start: 0.8826 (mtm) cc_final: 0.8575 (mtm) REVERT: H 446 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: I 28 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: I 208 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8407 (tttt) REVERT: I 446 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8299 (mp0) REVERT: J 28 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: J 285 TYR cc_start: 0.9122 (OUTLIER) cc_final: 0.7944 (t80) REVERT: J 441 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8531 (mp10) REVERT: K 28 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: K 285 TYR cc_start: 0.9197 (OUTLIER) cc_final: 0.8606 (t80) REVERT: K 292 MET cc_start: 0.8816 (mtm) cc_final: 0.8566 (mtm) REVERT: L 208 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8421 (tttm) REVERT: L 441 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8396 (mp10) outliers start: 95 outliers final: 50 residues processed: 465 average time/residue: 0.5084 time to fit residues: 289.6638 Evaluate side-chains 448 residues out of total 4644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 365 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 208 LYS Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 446 GLU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 414 THR Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain H residue 16 LYS Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 446 GLU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 208 LYS Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 446 GLU Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 414 THR Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 113 SER Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 441 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 124 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 140 optimal weight: 20.0000 chunk 316 optimal weight: 3.9990 chunk 3 optimal weight: 0.0170 chunk 49 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 367 optimal weight: 3.9990 chunk 353 optimal weight: 2.9990 chunk 410 optimal weight: 20.0000 overall best weight: 2.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN B 95 ASN C 95 ASN D 95 ASN E 95 ASN F 95 ASN G 95 ASN I 95 ASN J 95 ASN K 95 ASN L 95 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.141004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.102685 restraints weight = 150906.168| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.54 r_work: 0.2974 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 44364 Z= 0.218 Angle : 0.709 6.652 60192 Z= 0.389 Chirality : 0.047 0.139 6732 Planarity : 0.005 0.053 7560 Dihedral : 7.254 53.410 6456 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.97 % Allowed : 19.44 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.11), residues: 5388 helix: 2.94 (0.13), residues: 1656 sheet: 1.03 (0.15), residues: 1020 loop : -1.51 (0.10), residues: 2712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 221 TYR 0.016 0.002 TYR B 150 PHE 0.024 0.002 PHE C 183 TRP 0.009 0.001 TRP F 175 HIS 0.006 0.002 HIS J 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.22 (44328) covalent geometry : angle 0.70931 / 0.39 (60192) hydrogen bonds : bond 0.08313 / 5.66 ( 1884) hydrogen bonds : angle 4.91756 / 3.39 ( 5412) metal coordination : bond 0.00696 / 0.44 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17448.10 seconds wall clock time: 296 minutes 27.33 seconds (17787.33 seconds total)