Starting phenix.real_space_refine on Sat Feb 24 18:26:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lw1_23544/02_2024/7lw1_23544_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lw1_23544/02_2024/7lw1_23544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lw1_23544/02_2024/7lw1_23544.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lw1_23544/02_2024/7lw1_23544.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lw1_23544/02_2024/7lw1_23544_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lw1_23544/02_2024/7lw1_23544_trim_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.334 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: 6 Type Number sf(0) Gaussians P 20 5.49 5 S 148 5.16 5 C 14464 2.51 5 N 4052 2.21 5 O 4404 1.98 5 H 22704 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 26": "OD1" <-> "OD2" Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 53": "OE1" <-> "OE2" Residue "A TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 173": "OD1" <-> "OD2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "A ASP 190": "OD1" <-> "OD2" Residue "A PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A ASP 237": "OD1" <-> "OD2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 330": "OD1" <-> "OD2" Residue "A ASP 363": "OD1" <-> "OD2" Residue "A GLU 369": "OE1" <-> "OE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 515": "OE1" <-> "OE2" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 550": "OE1" <-> "OE2" Residue "A GLU 570": "OE1" <-> "OE2" Residue "A ASP 603": "OD1" <-> "OD2" Residue "A GLU 609": "OE1" <-> "OE2" Residue "A ASP 618": "OD1" <-> "OD2" Residue "A ASP 632": "OD1" <-> "OD2" Residue "A TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 688": "OE1" <-> "OE2" Residue "A GLU 692": "OE1" <-> "OE2" Residue "D ASP 26": "OD1" <-> "OD2" Residue "D TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 53": "OE1" <-> "OE2" Residue "D TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D GLU 137": "OE1" <-> "OE2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 173": "OD1" <-> "OD2" Residue "D ASP 179": "OD1" <-> "OD2" Residue "D ASP 190": "OD1" <-> "OD2" Residue "D PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D ASP 237": "OD1" <-> "OD2" Residue "D PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 245": "OE1" <-> "OE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 290": "OD1" <-> "OD2" Residue "D PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 330": "OD1" <-> "OD2" Residue "D ASP 363": "OD1" <-> "OD2" Residue "D GLU 369": "OE1" <-> "OE2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 515": "OE1" <-> "OE2" Residue "D PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 550": "OE1" <-> "OE2" Residue "D GLU 570": "OE1" <-> "OE2" Residue "D ASP 603": "OD1" <-> "OD2" Residue "D GLU 609": "OE1" <-> "OE2" Residue "D ASP 618": "OD1" <-> "OD2" Residue "D ASP 632": "OD1" <-> "OD2" Residue "D TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 688": "OE1" <-> "OE2" Residue "D GLU 692": "OE1" <-> "OE2" Residue "E ASP 26": "OD1" <-> "OD2" Residue "E TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 53": "OE1" <-> "OE2" Residue "E TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E GLU 137": "OE1" <-> "OE2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "E PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 173": "OD1" <-> "OD2" Residue "E ASP 179": "OD1" <-> "OD2" Residue "E ASP 190": "OD1" <-> "OD2" Residue "E PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 232": "OE1" <-> "OE2" Residue "E ASP 237": "OD1" <-> "OD2" Residue "E PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 245": "OE1" <-> "OE2" Residue "E GLU 249": "OE1" <-> "OE2" Residue "E ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 290": "OD1" <-> "OD2" Residue "E PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 330": "OD1" <-> "OD2" Residue "E ASP 363": "OD1" <-> "OD2" Residue "E GLU 369": "OE1" <-> "OE2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 440": "OE1" <-> "OE2" Residue "E TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 515": "OE1" <-> "OE2" Residue "E PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 550": "OE1" <-> "OE2" Residue "E GLU 570": "OE1" <-> "OE2" Residue "E ASP 603": "OD1" <-> "OD2" Residue "E GLU 609": "OE1" <-> "OE2" Residue "E ASP 618": "OD1" <-> "OD2" Residue "E ASP 632": "OD1" <-> "OD2" Residue "E TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 688": "OE1" <-> "OE2" Residue "E GLU 692": "OE1" <-> "OE2" Residue "F ASP 26": "OD1" <-> "OD2" Residue "F TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "F GLU 137": "OE1" <-> "OE2" Residue "F GLU 147": "OE1" <-> "OE2" Residue "F PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 173": "OD1" <-> "OD2" Residue "F ASP 179": "OD1" <-> "OD2" Residue "F ASP 190": "OD1" <-> "OD2" Residue "F PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 232": "OE1" <-> "OE2" Residue "F ASP 237": "OD1" <-> "OD2" Residue "F PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 245": "OE1" <-> "OE2" Residue "F GLU 249": "OE1" <-> "OE2" Residue "F ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 290": "OD1" <-> "OD2" Residue "F PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 330": "OD1" <-> "OD2" Residue "F ASP 363": "OD1" <-> "OD2" Residue "F GLU 369": "OE1" <-> "OE2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "F TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 515": "OE1" <-> "OE2" Residue "F PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 550": "OE1" <-> "OE2" Residue "F GLU 570": "OE1" <-> "OE2" Residue "F ASP 603": "OD1" <-> "OD2" Residue "F GLU 609": "OE1" <-> "OE2" Residue "F ASP 618": "OD1" <-> "OD2" Residue "F ASP 632": "OD1" <-> "OD2" Residue "F TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 688": "OE1" <-> "OE2" Residue "F GLU 692": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 45792 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 11355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 11355 Classifications: {'peptide': 744} Link IDs: {'PTRANS': 20, 'TRANS': 723} Chain: "D" Number of atoms: 11355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 11355 Classifications: {'peptide': 744} Link IDs: {'PTRANS': 20, 'TRANS': 723} Chain: "E" Number of atoms: 11355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 11355 Classifications: {'peptide': 744} Link IDs: {'PTRANS': 20, 'TRANS': 723} Chain: "F" Number of atoms: 11355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 11355 Classifications: {'peptide': 744} Link IDs: {'PTRANS': 20, 'TRANS': 723} Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {'ADP': 1, 'F6P': 1, 'FBP': 1, 'YG1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {'ADP': 1, 'F6P': 1, 'FBP': 1, 'YG1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {'ADP': 1, 'F6P': 1, 'FBP': 1, 'YG1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {'ADP': 1, 'F6P': 1, 'FBP': 1, 'YG1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1' ADP A 804 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP A 804 " occ=0.50 residue: pdb=" C1' ADP D 804 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP D 804 " occ=0.50 residue: pdb=" C1' ADP E 804 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP E 804 " occ=0.50 residue: pdb=" C1' ADP F 804 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP F 804 " occ=0.50 Time building chain proxies: 20.91, per 1000 atoms: 0.46 Number of scatterers: 45792 At special positions: 0 Unit cell: (158.55, 127.05, 129.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 148 16.00 P 20 15.00 O 4404 8.00 N 4052 7.00 C 14464 6.00 H 22704 1.00 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 - 3.50 Amino acid : False - 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: 41.86 Conformation dependent library (CDL) restraints added in 5.3 seconds 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5312 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 16 sheets defined 46.4% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.21 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 95 through 108 removed outlier: 3.902A pdb=" N ALA A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.643A pdb=" N ALA A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 147 through 152 Processing helix chain 'A' and resid 178 through 199 removed outlier: 4.366A pdb=" N THR A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 239 through 252 removed outlier: 3.576A pdb=" N ARG A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 298 through 301 Processing helix chain 'A' and resid 307 through 326 Processing helix chain 'A' and resid 348 through 363 removed outlier: 3.662A pdb=" N VAL A 358 " --> pdb=" O MET A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 374 Processing helix chain 'A' and resid 376 through 390 Processing helix chain 'A' and resid 414 through 427 Processing helix chain 'A' and resid 438 through 444 Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 473 through 487 removed outlier: 6.465A pdb=" N GLU A 478 " --> pdb=" O GLY A 475 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL A 481 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR A 487 " --> pdb=" O ILE A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 510 removed outlier: 3.794A pdb=" N ALA A 510 " --> pdb=" O GLN A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 561 removed outlier: 3.576A pdb=" N SER A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 554 " --> pdb=" O GLU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 Processing helix chain 'A' and resid 601 through 616 removed outlier: 3.742A pdb=" N MET A 615 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS A 616 " --> pdb=" O THR A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 646 Processing helix chain 'A' and resid 660 through 663 Processing helix chain 'A' and resid 669 through 691 Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'A' and resid 724 through 728 removed outlier: 3.961A pdb=" N LYS A 727 " --> pdb=" O GLU A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 751 removed outlier: 3.923A pdb=" N SER A 743 " --> pdb=" O TRP A 740 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 748 " --> pdb=" O ARG A 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 95 through 108 removed outlier: 3.902A pdb=" N ALA D 100 " --> pdb=" O GLU D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.643A pdb=" N ALA D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 141 Processing helix chain 'D' and resid 147 through 152 Processing helix chain 'D' and resid 178 through 199 removed outlier: 4.365A pdb=" N THR D 194 " --> pdb=" O ASP D 190 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR D 195 " --> pdb=" O ALA D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 223 Processing helix chain 'D' and resid 231 through 233 No H-bonds generated for 'chain 'D' and resid 231 through 233' Processing helix chain 'D' and resid 239 through 252 removed outlier: 3.576A pdb=" N ARG D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 287 Processing helix chain 'D' and resid 298 through 301 Processing helix chain 'D' and resid 307 through 326 Processing helix chain 'D' and resid 348 through 363 removed outlier: 3.661A pdb=" N VAL D 358 " --> pdb=" O MET D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 374 Processing helix chain 'D' and resid 376 through 390 Processing helix chain 'D' and resid 414 through 427 Processing helix chain 'D' and resid 438 through 444 Processing helix chain 'D' and resid 453 through 455 No H-bonds generated for 'chain 'D' and resid 453 through 455' Processing helix chain 'D' and resid 473 through 487 removed outlier: 6.466A pdb=" N GLU D 478 " --> pdb=" O GLY D 475 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL D 481 " --> pdb=" O GLU D 478 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR D 487 " --> pdb=" O ILE D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 510 removed outlier: 3.794A pdb=" N ALA D 510 " --> pdb=" O GLN D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 561 removed outlier: 3.576A pdb=" N SER D 551 " --> pdb=" O ALA D 547 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG D 554 " --> pdb=" O GLU D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 587 Processing helix chain 'D' and resid 601 through 616 removed outlier: 3.742A pdb=" N MET D 615 " --> pdb=" O MET D 611 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS D 616 " --> pdb=" O THR D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 646 Processing helix chain 'D' and resid 660 through 663 Processing helix chain 'D' and resid 669 through 691 Processing helix chain 'D' and resid 704 through 706 No H-bonds generated for 'chain 'D' and resid 704 through 706' Processing helix chain 'D' and resid 724 through 728 removed outlier: 3.961A pdb=" N LYS D 727 " --> pdb=" O GLU D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 751 removed outlier: 3.924A pdb=" N SER D 743 " --> pdb=" O TRP D 740 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 748 " --> pdb=" O ARG D 745 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 43 Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 95 through 108 removed outlier: 3.902A pdb=" N ALA E 100 " --> pdb=" O GLU E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 130 removed outlier: 3.643A pdb=" N ALA E 125 " --> pdb=" O SER E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 141 Processing helix chain 'E' and resid 147 through 152 Processing helix chain 'E' and resid 178 through 199 removed outlier: 4.366A pdb=" N THR E 194 " --> pdb=" O ASP E 190 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR E 195 " --> pdb=" O ALA E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 223 Processing helix chain 'E' and resid 231 through 233 No H-bonds generated for 'chain 'E' and resid 231 through 233' Processing helix chain 'E' and resid 239 through 252 removed outlier: 3.577A pdb=" N ARG E 251 " --> pdb=" O LEU E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 287 Processing helix chain 'E' and resid 298 through 301 Processing helix chain 'E' and resid 307 through 326 Processing helix chain 'E' and resid 348 through 363 removed outlier: 3.662A pdb=" N VAL E 358 " --> pdb=" O MET E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 374 Processing helix chain 'E' and resid 376 through 390 Processing helix chain 'E' and resid 414 through 427 Processing helix chain 'E' and resid 438 through 444 Processing helix chain 'E' and resid 453 through 455 No H-bonds generated for 'chain 'E' and resid 453 through 455' Processing helix chain 'E' and resid 473 through 487 removed outlier: 6.465A pdb=" N GLU E 478 " --> pdb=" O GLY E 475 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL E 481 " --> pdb=" O GLU E 478 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR E 487 " --> pdb=" O ILE E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 510 removed outlier: 3.794A pdb=" N ALA E 510 " --> pdb=" O GLN E 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 561 removed outlier: 3.577A pdb=" N SER E 551 " --> pdb=" O ALA E 547 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG E 554 " --> pdb=" O GLU E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 587 Processing helix chain 'E' and resid 601 through 616 removed outlier: 3.741A pdb=" N MET E 615 " --> pdb=" O MET E 611 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS E 616 " --> pdb=" O THR E 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 636 through 646 Processing helix chain 'E' and resid 660 through 663 Processing helix chain 'E' and resid 669 through 691 Processing helix chain 'E' and resid 704 through 706 No H-bonds generated for 'chain 'E' and resid 704 through 706' Processing helix chain 'E' and resid 724 through 728 removed outlier: 3.961A pdb=" N LYS E 727 " --> pdb=" O GLU E 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 740 through 751 removed outlier: 3.923A pdb=" N SER E 743 " --> pdb=" O TRP E 740 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E 748 " --> pdb=" O ARG E 745 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 43 Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 95 through 108 removed outlier: 3.902A pdb=" N ALA F 100 " --> pdb=" O GLU F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 130 removed outlier: 3.643A pdb=" N ALA F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 141 Processing helix chain 'F' and resid 147 through 152 Processing helix chain 'F' and resid 178 through 199 removed outlier: 4.365A pdb=" N THR F 194 " --> pdb=" O ASP F 190 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR F 195 " --> pdb=" O ALA F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 223 Processing helix chain 'F' and resid 231 through 233 No H-bonds generated for 'chain 'F' and resid 231 through 233' Processing helix chain 'F' and resid 239 through 252 removed outlier: 3.577A pdb=" N ARG F 251 " --> pdb=" O LEU F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 287 Processing helix chain 'F' and resid 298 through 301 Processing helix chain 'F' and resid 307 through 326 Processing helix chain 'F' and resid 348 through 363 removed outlier: 3.662A pdb=" N VAL F 358 " --> pdb=" O MET F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 374 Processing helix chain 'F' and resid 376 through 390 Processing helix chain 'F' and resid 414 through 427 Processing helix chain 'F' and resid 438 through 444 Processing helix chain 'F' and resid 453 through 455 No H-bonds generated for 'chain 'F' and resid 453 through 455' Processing helix chain 'F' and resid 473 through 487 removed outlier: 6.465A pdb=" N GLU F 478 " --> pdb=" O GLY F 475 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL F 481 " --> pdb=" O GLU F 478 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR F 487 " --> pdb=" O ILE F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 510 removed outlier: 3.794A pdb=" N ALA F 510 " --> pdb=" O GLN F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 561 removed outlier: 3.576A pdb=" N SER F 551 " --> pdb=" O ALA F 547 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG F 554 " --> pdb=" O GLU F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 587 Processing helix chain 'F' and resid 601 through 616 removed outlier: 3.742A pdb=" N MET F 615 " --> pdb=" O MET F 611 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS F 616 " --> pdb=" O THR F 612 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 646 Processing helix chain 'F' and resid 660 through 663 Processing helix chain 'F' and resid 669 through 691 Processing helix chain 'F' and resid 704 through 706 No H-bonds generated for 'chain 'F' and resid 704 through 706' Processing helix chain 'F' and resid 724 through 728 removed outlier: 3.961A pdb=" N LYS F 727 " --> pdb=" O GLU F 724 " (cutoff:3.500A) Processing helix chain 'F' and resid 740 through 751 removed outlier: 3.923A pdb=" N SER F 743 " --> pdb=" O TRP F 740 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU F 748 " --> pdb=" O ARG F 745 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 342 through 347 removed outlier: 4.203A pdb=" N GLN A 342 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS A 334 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A 162 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LEU A 338 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS A 47 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL A 20 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE A 49 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR A 22 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE A 51 " --> pdb=" O THR A 22 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 291 through 295 removed outlier: 6.468A pdb=" N THR A 202 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N THR A 294 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A 204 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN A 258 " --> pdb=" O PHE A 203 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU A 205 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE A 260 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL A 207 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 262 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP A 227 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ALA A 263 " --> pdb=" O TRP A 227 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N PHE A 229 " --> pdb=" O ALA A 263 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 717 through 721 removed outlier: 6.466A pdb=" N MET A 521 " --> pdb=" O CYS A 708 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ILE A 710 " --> pdb=" O MET A 521 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL A 523 " --> pdb=" O ILE A 710 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N LEU A 712 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR A 431 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE A 404 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR A 433 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N ASN A 406 " --> pdb=" O TYR A 433 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL A 435 " --> pdb=" O ASN A 406 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 652 through 657 removed outlier: 6.318A pdb=" N ALA A 591 " --> pdb=" O LEU A 625 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ASN A 627 " --> pdb=" O ALA A 591 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TYR A 593 " --> pdb=" O ASN A 627 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 342 through 347 removed outlier: 4.203A pdb=" N GLN D 342 " --> pdb=" O SER D 339 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS D 334 " --> pdb=" O ILE D 158 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL D 162 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LEU D 338 " --> pdb=" O VAL D 162 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS D 47 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL D 20 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE D 49 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N THR D 22 " --> pdb=" O PHE D 49 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ILE D 51 " --> pdb=" O THR D 22 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 291 through 295 removed outlier: 6.468A pdb=" N THR D 202 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N THR D 294 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL D 204 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASN D 258 " --> pdb=" O PHE D 203 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU D 205 " --> pdb=" O ASN D 258 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE D 260 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL D 207 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE D 262 " --> pdb=" O VAL D 207 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP D 227 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ALA D 263 " --> pdb=" O TRP D 227 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N PHE D 229 " --> pdb=" O ALA D 263 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 717 through 721 removed outlier: 6.467A pdb=" N MET D 521 " --> pdb=" O CYS D 708 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ILE D 710 " --> pdb=" O MET D 521 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL D 523 " --> pdb=" O ILE D 710 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N LEU D 712 " --> pdb=" O VAL D 523 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR D 431 " --> pdb=" O LEU D 402 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE D 404 " --> pdb=" O THR D 431 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR D 433 " --> pdb=" O ILE D 404 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N ASN D 406 " --> pdb=" O TYR D 433 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N VAL D 435 " --> pdb=" O ASN D 406 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 652 through 657 removed outlier: 6.318A pdb=" N ALA D 591 " --> pdb=" O LEU D 625 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ASN D 627 " --> pdb=" O ALA D 591 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TYR D 593 " --> pdb=" O ASN D 627 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 342 through 347 removed outlier: 4.203A pdb=" N GLN E 342 " --> pdb=" O SER E 339 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS E 334 " --> pdb=" O ILE E 158 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL E 162 " --> pdb=" O VAL E 336 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N LEU E 338 " --> pdb=" O VAL E 162 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS E 47 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL E 20 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE E 49 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N THR E 22 " --> pdb=" O PHE E 49 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE E 51 " --> pdb=" O THR E 22 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 291 through 295 removed outlier: 6.468A pdb=" N THR E 202 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N THR E 294 " --> pdb=" O THR E 202 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL E 204 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASN E 258 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU E 205 " --> pdb=" O ASN E 258 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE E 260 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL E 207 " --> pdb=" O ILE E 260 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE E 262 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP E 227 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ALA E 263 " --> pdb=" O TRP E 227 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N PHE E 229 " --> pdb=" O ALA E 263 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'E' and resid 717 through 721 removed outlier: 6.466A pdb=" N MET E 521 " --> pdb=" O CYS E 708 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ILE E 710 " --> pdb=" O MET E 521 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL E 523 " --> pdb=" O ILE E 710 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N LEU E 712 " --> pdb=" O VAL E 523 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR E 431 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE E 404 " --> pdb=" O THR E 431 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR E 433 " --> pdb=" O ILE E 404 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N ASN E 406 " --> pdb=" O TYR E 433 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N VAL E 435 " --> pdb=" O ASN E 406 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 652 through 657 removed outlier: 6.317A pdb=" N ALA E 591 " --> pdb=" O LEU E 625 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ASN E 627 " --> pdb=" O ALA E 591 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TYR E 593 " --> pdb=" O ASN E 627 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 342 through 347 removed outlier: 4.203A pdb=" N GLN F 342 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS F 334 " --> pdb=" O ILE F 158 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL F 162 " --> pdb=" O VAL F 336 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LEU F 338 " --> pdb=" O VAL F 162 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS F 47 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL F 20 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE F 49 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR F 22 " --> pdb=" O PHE F 49 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ILE F 51 " --> pdb=" O THR F 22 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 291 through 295 removed outlier: 6.468A pdb=" N THR F 202 " --> pdb=" O ARG F 292 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N THR F 294 " --> pdb=" O THR F 202 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL F 204 " --> pdb=" O THR F 294 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN F 258 " --> pdb=" O PHE F 203 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU F 205 " --> pdb=" O ASN F 258 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE F 260 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL F 207 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE F 262 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP F 227 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ALA F 263 " --> pdb=" O TRP F 227 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N PHE F 229 " --> pdb=" O ALA F 263 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'F' and resid 717 through 721 removed outlier: 6.466A pdb=" N MET F 521 " --> pdb=" O CYS F 708 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ILE F 710 " --> pdb=" O MET F 521 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL F 523 " --> pdb=" O ILE F 710 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N LEU F 712 " --> pdb=" O VAL F 523 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR F 431 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE F 404 " --> pdb=" O THR F 431 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR F 433 " --> pdb=" O ILE F 404 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N ASN F 406 " --> pdb=" O TYR F 433 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N VAL F 435 " --> pdb=" O ASN F 406 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 652 through 657 removed outlier: 6.318A pdb=" N ALA F 591 " --> pdb=" O LEU F 625 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ASN F 627 " --> pdb=" O ALA F 591 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TYR F 593 " --> pdb=" O ASN F 627 " (cutoff:3.500A) 1040 hydrogen bonds defined for protein. 2868 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: 19.90 Time building geometry restraints manager: 42.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.09: 15394 1.09 - 1.27: 11082 1.27 - 1.45: 6743 1.45 - 1.64: 12761 1.64 - 1.82: 240 Bond restraints: 46220 Sorted by residual: bond pdb=" C5 FBP A 802 " pdb=" O5 FBP A 802 " ideal model delta sigma weight residual 1.608 1.417 0.191 2.00e-02 2.50e+03 9.08e+01 bond pdb=" C5 FBP D 802 " pdb=" O5 FBP D 802 " ideal model delta sigma weight residual 1.608 1.417 0.191 2.00e-02 2.50e+03 9.08e+01 bond pdb=" C5 FBP F 802 " pdb=" O5 FBP F 802 " ideal model delta sigma weight residual 1.608 1.417 0.191 2.00e-02 2.50e+03 9.08e+01 bond pdb=" C5 FBP E 802 " pdb=" O5 FBP E 802 " ideal model delta sigma weight residual 1.608 1.417 0.191 2.00e-02 2.50e+03 9.07e+01 bond pdb=" C2 F6P E 803 " pdb=" O5 F6P E 803 " ideal model delta sigma weight residual 1.600 1.418 0.182 2.00e-02 2.50e+03 8.24e+01 ... (remaining 46215 not shown) Histogram of bond angle deviations from ideal: 73.12 - 94.49: 84 94.49 - 115.86: 55976 115.86 - 137.24: 27208 137.24 - 158.61: 4 158.61 - 179.98: 8 Bond angle restraints: 83280 Sorted by residual: angle pdb=" CG2 VAL E 162 " pdb=" CB VAL E 162 " pdb=" HB VAL E 162 " ideal model delta sigma weight residual 108.00 73.12 34.88 3.00e+00 1.11e-01 1.35e+02 angle pdb=" CG2 VAL D 162 " pdb=" CB VAL D 162 " pdb=" HB VAL D 162 " ideal model delta sigma weight residual 108.00 73.16 34.84 3.00e+00 1.11e-01 1.35e+02 angle pdb=" CG2 VAL A 162 " pdb=" CB VAL A 162 " pdb=" HB VAL A 162 " ideal model delta sigma weight residual 108.00 73.16 34.84 3.00e+00 1.11e-01 1.35e+02 angle pdb=" CG2 VAL F 162 " pdb=" CB VAL F 162 " pdb=" HB VAL F 162 " ideal model delta sigma weight residual 108.00 73.19 34.81 3.00e+00 1.11e-01 1.35e+02 angle pdb=" CA VAL E 709 " pdb=" CB VAL E 709 " pdb=" CG1 VAL E 709 " ideal model delta sigma weight residual 110.40 129.88 -19.48 1.70e+00 3.46e-01 1.31e+02 ... (remaining 83275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 20661 35.70 - 71.41: 959 71.41 - 107.11: 70 107.11 - 142.81: 5 142.81 - 178.52: 5 Dihedral angle restraints: 21700 sinusoidal: 12052 harmonic: 9648 Sorted by residual: dihedral pdb=" O1B ADP E 804 " pdb=" O3A ADP E 804 " pdb=" PB ADP E 804 " pdb=" PA ADP E 804 " ideal model delta sinusoidal sigma weight residual 300.00 143.89 156.11 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" O1B ADP A 804 " pdb=" O3A ADP A 804 " pdb=" PB ADP A 804 " pdb=" PA ADP A 804 " ideal model delta sinusoidal sigma weight residual 300.00 143.89 156.11 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" C5' ADP E 804 " pdb=" O5' ADP E 804 " pdb=" PA ADP E 804 " pdb=" O2A ADP E 804 " ideal model delta sinusoidal sigma weight residual 300.00 157.54 142.46 1 2.00e+01 2.50e-03 4.30e+01 ... (remaining 21697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.240: 3433 0.240 - 0.480: 111 0.480 - 0.720: 0 0.720 - 0.960: 12 0.960 - 1.200: 4 Chirality restraints: 3560 Sorted by residual: chirality pdb=" CB VAL E 709 " pdb=" CA VAL E 709 " pdb=" CG1 VAL E 709 " pdb=" CG2 VAL E 709 " both_signs ideal model delta sigma weight residual False -2.63 -1.43 -1.20 2.00e-01 2.50e+01 3.60e+01 chirality pdb=" CB VAL D 709 " pdb=" CA VAL D 709 " pdb=" CG1 VAL D 709 " pdb=" CG2 VAL D 709 " both_signs ideal model delta sigma weight residual False -2.63 -1.43 -1.20 2.00e-01 2.50e+01 3.60e+01 chirality pdb=" CB VAL F 709 " pdb=" CA VAL F 709 " pdb=" CG1 VAL F 709 " pdb=" CG2 VAL F 709 " both_signs ideal model delta sigma weight residual False -2.63 -1.43 -1.20 2.00e-01 2.50e+01 3.60e+01 ... (remaining 3557 not shown) Planarity restraints: 6956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 654 " -0.135 9.50e-02 1.11e+02 1.15e-01 2.53e+02 pdb=" NE ARG F 654 " -0.079 2.00e-02 2.50e+03 pdb=" CZ ARG F 654 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG F 654 " 0.058 2.00e-02 2.50e+03 pdb=" NH2 ARG F 654 " 0.017 2.00e-02 2.50e+03 pdb="HH11 ARG F 654 " 0.151 2.00e-02 2.50e+03 pdb="HH12 ARG F 654 " -0.233 2.00e-02 2.50e+03 pdb="HH21 ARG F 654 " -0.019 2.00e-02 2.50e+03 pdb="HH22 ARG F 654 " 0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 654 " 0.135 9.50e-02 1.11e+02 1.15e-01 2.53e+02 pdb=" NE ARG D 654 " 0.079 2.00e-02 2.50e+03 pdb=" CZ ARG D 654 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG D 654 " -0.058 2.00e-02 2.50e+03 pdb=" NH2 ARG D 654 " -0.017 2.00e-02 2.50e+03 pdb="HH11 ARG D 654 " -0.151 2.00e-02 2.50e+03 pdb="HH12 ARG D 654 " 0.233 2.00e-02 2.50e+03 pdb="HH21 ARG D 654 " 0.019 2.00e-02 2.50e+03 pdb="HH22 ARG D 654 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 654 " -0.135 9.50e-02 1.11e+02 1.15e-01 2.53e+02 pdb=" NE ARG E 654 " -0.080 2.00e-02 2.50e+03 pdb=" CZ ARG E 654 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG E 654 " 0.058 2.00e-02 2.50e+03 pdb=" NH2 ARG E 654 " 0.017 2.00e-02 2.50e+03 pdb="HH11 ARG E 654 " 0.151 2.00e-02 2.50e+03 pdb="HH12 ARG E 654 " -0.233 2.00e-02 2.50e+03 pdb="HH21 ARG E 654 " -0.019 2.00e-02 2.50e+03 pdb="HH22 ARG E 654 " 0.113 2.00e-02 2.50e+03 ... (remaining 6953 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.03: 1308 2.03 - 2.67: 59756 2.67 - 3.31: 144505 3.31 - 3.96: 193933 3.96 - 4.60: 289113 Nonbonded interactions: 688615 Sorted by model distance: nonbonded pdb="HH22 ARG F 734 " pdb=" O5P FBP F 802 " model vdw 1.384 1.850 nonbonded pdb="HH22 ARG E 734 " pdb=" O4P FBP E 802 " model vdw 1.384 1.850 nonbonded pdb="HH22 ARG A 734 " pdb=" O4P FBP A 802 " model vdw 1.384 1.850 nonbonded pdb="HH22 ARG D 734 " pdb=" O5P FBP D 802 " model vdw 1.385 1.850 nonbonded pdb=" HG SER D 121 " pdb=" O1B ADP D 804 " model vdw 1.393 1.850 ... (remaining 688610 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.700 Extract box with map and model: 8.290 Check model and map are aligned: 0.680 Set scattering table: 0.410 Process input model: 156.680 Find NCS groups from input model: 2.400 Set up NCS constraints: 0.260 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:14.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 185.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 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 : 0.014 0.191 23516 Z= 0.965 Angle : 2.111 19.484 31844 Z= 1.354 Chirality : 0.123 1.200 3560 Planarity : 0.016 0.163 4064 Dihedral : 16.963 178.516 8744 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.45 % Favored : 95.42 % Rotamer: Outliers : 1.00 % Allowed : 4.68 % Favored : 94.31 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.14), residues: 2968 helix: -1.86 (0.11), residues: 1412 sheet: -0.04 (0.25), residues: 348 loop : -0.17 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.109 0.024 TRP D 458 HIS 0.011 0.004 HIS D 211 PHE 0.088 0.016 PHE D 169 TYR 0.195 0.024 TYR E 754 ARG 0.013 0.002 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 594 time to evaluate : 3.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.8159 (t80) cc_final: 0.7877 (t80) REVERT: A 293 VAL cc_start: 0.8842 (p) cc_final: 0.8559 (p) REVERT: A 346 LEU cc_start: 0.8035 (mt) cc_final: 0.7795 (mt) REVERT: A 349 MET cc_start: 0.6160 (mmm) cc_final: 0.5687 (mmm) REVERT: A 353 GLN cc_start: 0.7120 (mm-40) cc_final: 0.6743 (mm-40) REVERT: A 448 GLN cc_start: 0.7833 (pt0) cc_final: 0.7505 (pt0) REVERT: A 485 ARG cc_start: 0.6842 (ttm170) cc_final: 0.6321 (ttm110) REVERT: A 743 SER cc_start: 0.8585 (p) cc_final: 0.8329 (m) REVERT: D 43 TYR cc_start: 0.8142 (t80) cc_final: 0.7911 (t80) REVERT: D 293 VAL cc_start: 0.8846 (p) cc_final: 0.8497 (p) REVERT: D 346 LEU cc_start: 0.8045 (mt) cc_final: 0.7810 (mt) REVERT: D 349 MET cc_start: 0.6196 (mmm) cc_final: 0.5775 (mmm) REVERT: D 353 GLN cc_start: 0.7165 (mm-40) cc_final: 0.6769 (mm-40) REVERT: D 448 GLN cc_start: 0.7861 (pt0) cc_final: 0.7496 (pt0) REVERT: E 43 TYR cc_start: 0.8136 (t80) cc_final: 0.7921 (t80) REVERT: E 56 GLU cc_start: 0.6647 (tm-30) cc_final: 0.6118 (tm-30) REVERT: E 293 VAL cc_start: 0.8847 (p) cc_final: 0.8568 (p) REVERT: E 346 LEU cc_start: 0.8069 (mt) cc_final: 0.7817 (mt) REVERT: E 349 MET cc_start: 0.6178 (mmm) cc_final: 0.5701 (mmm) REVERT: E 353 GLN cc_start: 0.7127 (mm-40) cc_final: 0.6737 (mm-40) REVERT: E 448 GLN cc_start: 0.7799 (pt0) cc_final: 0.7474 (pt0) REVERT: E 602 HIS cc_start: 0.6717 (t70) cc_final: 0.6472 (t-170) REVERT: F 43 TYR cc_start: 0.8150 (t80) cc_final: 0.7843 (t80) REVERT: F 293 VAL cc_start: 0.8848 (p) cc_final: 0.8557 (p) REVERT: F 346 LEU cc_start: 0.8062 (mt) cc_final: 0.7827 (mt) REVERT: F 349 MET cc_start: 0.6196 (mmm) cc_final: 0.5746 (mmm) REVERT: F 353 GLN cc_start: 0.7120 (mm-40) cc_final: 0.6768 (mm-40) REVERT: F 448 GLN cc_start: 0.7828 (pt0) cc_final: 0.7477 (pt0) REVERT: F 732 GLU cc_start: 0.6662 (tt0) cc_final: 0.6451 (tt0) REVERT: F 743 SER cc_start: 0.8560 (p) cc_final: 0.8318 (m) outliers start: 24 outliers final: 8 residues processed: 618 average time/residue: 2.2449 time to fit residues: 1659.8482 Evaluate side-chains 445 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 437 time to evaluate : 3.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 363 ASP Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain F residue 601 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 0.9990 chunk 224 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 151 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 232 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 172 optimal weight: 0.9990 chunk 268 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 285 GLN A 406 ASN A 476 GLN A 607 ASN A 620 GLN A 641 ASN A 660 HIS D 406 ASN D 476 GLN D 607 ASN D 620 GLN D 641 ASN E 67 GLN E 69 ASN E 75 ASN E 406 ASN E 476 GLN E 607 ASN E 620 GLN E 641 ASN E 660 HIS F 69 ASN F 75 ASN F 383 ASN F 406 ASN F 476 GLN F 607 ASN F 641 ASN F 660 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23516 Z= 0.264 Angle : 0.795 10.975 31844 Z= 0.415 Chirality : 0.103 1.427 3560 Planarity : 0.005 0.063 4064 Dihedral : 12.685 160.209 3559 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.47 % Allowed : 13.00 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 2968 helix: -0.34 (0.12), residues: 1424 sheet: -0.24 (0.23), residues: 432 loop : 0.15 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 685 HIS 0.010 0.002 HIS A 660 PHE 0.012 0.002 PHE A 651 TYR 0.019 0.002 TYR F 674 ARG 0.004 0.001 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 489 time to evaluate : 3.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7332 (m-30) REVERT: A 269 ARG cc_start: 0.6756 (tpt170) cc_final: 0.6418 (mmt180) REVERT: A 293 VAL cc_start: 0.8825 (p) cc_final: 0.8534 (p) REVERT: A 346 LEU cc_start: 0.7966 (mt) cc_final: 0.7759 (mt) REVERT: A 349 MET cc_start: 0.6246 (mmm) cc_final: 0.5787 (mmm) REVERT: A 353 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6792 (mm-40) REVERT: A 448 GLN cc_start: 0.7883 (pt0) cc_final: 0.7619 (pt0) REVERT: A 486 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7620 (mp) REVERT: A 564 ARG cc_start: 0.8180 (mtt-85) cc_final: 0.7974 (mtt-85) REVERT: A 601 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8458 (pp) REVERT: A 615 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.6985 (mpt) REVERT: D 346 LEU cc_start: 0.7983 (mt) cc_final: 0.7777 (mt) REVERT: D 349 MET cc_start: 0.6231 (mmm) cc_final: 0.5798 (mmm) REVERT: D 353 GLN cc_start: 0.7249 (mm-40) cc_final: 0.6807 (mm-40) REVERT: D 448 GLN cc_start: 0.7920 (pt0) cc_final: 0.7568 (pt0) REVERT: D 476 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7585 (mm110) REVERT: D 486 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7656 (mp) REVERT: D 601 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8435 (pp) REVERT: D 615 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.7097 (mpt) REVERT: D 727 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8119 (ptpp) REVERT: D 732 GLU cc_start: 0.6382 (tt0) cc_final: 0.6154 (tt0) REVERT: E 43 TYR cc_start: 0.8215 (t80) cc_final: 0.7981 (t80) REVERT: E 208 MET cc_start: 0.7602 (mtp) cc_final: 0.7400 (mtp) REVERT: E 226 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7354 (m-30) REVERT: E 293 VAL cc_start: 0.8835 (p) cc_final: 0.8546 (p) REVERT: E 316 MET cc_start: 0.8428 (mmp) cc_final: 0.8201 (mmp) REVERT: E 318 MET cc_start: 0.7726 (ttp) cc_final: 0.7518 (ttm) REVERT: E 346 LEU cc_start: 0.8032 (mt) cc_final: 0.7830 (mt) REVERT: E 349 MET cc_start: 0.6254 (mmm) cc_final: 0.5867 (mmt) REVERT: E 353 GLN cc_start: 0.7208 (mm-40) cc_final: 0.6778 (mm-40) REVERT: E 448 GLN cc_start: 0.7832 (pt0) cc_final: 0.7506 (pt0) REVERT: E 486 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7573 (mp) REVERT: E 564 ARG cc_start: 0.8180 (mtt-85) cc_final: 0.7958 (mtt-85) REVERT: E 601 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8315 (pp) REVERT: E 615 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.7013 (mpt) REVERT: E 727 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8157 (ptpp) REVERT: F 269 ARG cc_start: 0.6703 (tpt170) cc_final: 0.6383 (mmt180) REVERT: F 293 VAL cc_start: 0.8808 (p) cc_final: 0.8521 (p) REVERT: F 353 GLN cc_start: 0.7205 (mm-40) cc_final: 0.6807 (mm-40) REVERT: F 360 LYS cc_start: 0.7377 (mmmm) cc_final: 0.7097 (tppp) REVERT: F 448 GLN cc_start: 0.7894 (pt0) cc_final: 0.7614 (pt0) REVERT: F 486 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7644 (mp) REVERT: F 564 ARG cc_start: 0.8171 (mtt-85) cc_final: 0.7956 (mtt-85) REVERT: F 601 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8196 (pp) REVERT: F 615 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.7110 (mpt) outliers start: 59 outliers final: 13 residues processed: 527 average time/residue: 2.0022 time to fit residues: 1285.9364 Evaluate side-chains 468 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 439 time to evaluate : 3.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 727 LYS Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 486 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 615 MET Chi-restraints excluded: chain E residue 727 LYS Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 615 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 269 optimal weight: 3.9990 chunk 290 optimal weight: 1.9990 chunk 239 optimal weight: 0.9980 chunk 267 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 216 optimal weight: 0.3980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 69 ASN D 660 HIS F 476 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23516 Z= 0.297 Angle : 0.717 11.258 31844 Z= 0.368 Chirality : 0.107 1.509 3560 Planarity : 0.004 0.037 4064 Dihedral : 11.736 169.791 3557 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.97 % Allowed : 14.67 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 2968 helix: 0.15 (0.13), residues: 1468 sheet: -0.56 (0.22), residues: 464 loop : 0.12 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 685 HIS 0.008 0.001 HIS D 660 PHE 0.018 0.002 PHE A 651 TYR 0.013 0.001 TYR A 385 ARG 0.004 0.000 ARG F 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 470 time to evaluate : 3.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.8289 (t80) cc_final: 0.8082 (t80) REVERT: A 226 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7473 (m-30) REVERT: A 293 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8530 (p) REVERT: A 353 GLN cc_start: 0.7233 (mm-40) cc_final: 0.7019 (tm130) REVERT: A 365 LYS cc_start: 0.7724 (mmtm) cc_final: 0.7360 (mmmm) REVERT: A 448 GLN cc_start: 0.7900 (pt0) cc_final: 0.7552 (pt0) REVERT: A 486 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7663 (mp) REVERT: A 490 HIS cc_start: 0.8279 (m90) cc_final: 0.8013 (m90) REVERT: A 564 ARG cc_start: 0.8232 (mtt-85) cc_final: 0.7966 (mtt-85) REVERT: D 226 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7497 (m-30) REVERT: D 293 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8552 (p) REVERT: D 316 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7511 (mmp) REVERT: D 346 LEU cc_start: 0.8059 (mt) cc_final: 0.7853 (mt) REVERT: D 353 GLN cc_start: 0.7255 (mm-40) cc_final: 0.6831 (mm-40) REVERT: D 440 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7098 (tt0) REVERT: D 448 GLN cc_start: 0.7939 (pt0) cc_final: 0.7648 (pt0) REVERT: D 486 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7705 (mp) REVERT: D 490 HIS cc_start: 0.8277 (m90) cc_final: 0.8006 (m90) REVERT: D 615 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.7075 (mpt) REVERT: D 732 GLU cc_start: 0.6472 (tt0) cc_final: 0.6254 (tt0) REVERT: E 226 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7517 (m-30) REVERT: E 243 MET cc_start: 0.8257 (ttp) cc_final: 0.7764 (ttt) REVERT: E 285 GLN cc_start: 0.7141 (tm-30) cc_final: 0.6738 (tm130) REVERT: E 293 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8539 (p) REVERT: E 353 GLN cc_start: 0.7225 (mm-40) cc_final: 0.6798 (mm110) REVERT: E 448 GLN cc_start: 0.7858 (pt0) cc_final: 0.7547 (pt0) REVERT: E 486 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7651 (mp) REVERT: E 490 HIS cc_start: 0.8290 (m90) cc_final: 0.8027 (m90) REVERT: E 564 ARG cc_start: 0.8244 (mtt-85) cc_final: 0.7979 (mtt-85) REVERT: E 615 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.7099 (mpt) REVERT: F 226 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7480 (m-30) REVERT: F 243 MET cc_start: 0.8266 (ttp) cc_final: 0.7755 (ttt) REVERT: F 285 GLN cc_start: 0.7198 (tm-30) cc_final: 0.6884 (tm130) REVERT: F 293 VAL cc_start: 0.8840 (OUTLIER) cc_final: 0.8533 (p) REVERT: F 316 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7506 (mmp) REVERT: F 353 GLN cc_start: 0.7198 (mm-40) cc_final: 0.6786 (mm110) REVERT: F 448 GLN cc_start: 0.7897 (pt0) cc_final: 0.7642 (pt0) REVERT: F 478 GLU cc_start: 0.7077 (tp30) cc_final: 0.6865 (tp30) REVERT: F 486 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7687 (mp) REVERT: F 490 HIS cc_start: 0.8286 (m90) cc_final: 0.8058 (m90) REVERT: F 564 ARG cc_start: 0.8244 (mtt-85) cc_final: 0.7954 (mtt-85) REVERT: F 615 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.7104 (mpt) outliers start: 71 outliers final: 34 residues processed: 499 average time/residue: 2.1282 time to fit residues: 1280.8960 Evaluate side-chains 498 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 446 time to evaluate : 3.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 499 GLU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 322 MET Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 486 ILE Chi-restraints excluded: chain E residue 499 GLU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 615 MET Chi-restraints excluded: chain E residue 632 ASP Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 499 GLU Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 615 MET Chi-restraints excluded: chain F residue 632 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 270 optimal weight: 3.9990 chunk 286 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 383 ASN F 383 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 23516 Z= 0.306 Angle : 0.691 11.491 31844 Z= 0.353 Chirality : 0.107 1.533 3560 Planarity : 0.004 0.033 4064 Dihedral : 11.035 171.032 3556 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.05 % Allowed : 15.55 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 2968 helix: 0.37 (0.13), residues: 1472 sheet: -0.52 (0.22), residues: 480 loop : 0.29 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 132 HIS 0.003 0.001 HIS E 428 PHE 0.014 0.002 PHE D 599 TYR 0.012 0.001 TYR F 43 ARG 0.006 0.000 ARG F 513 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 463 time to evaluate : 3.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.8331 (t80) cc_final: 0.8124 (t80) REVERT: A 226 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7525 (m-30) REVERT: A 243 MET cc_start: 0.8315 (ttp) cc_final: 0.7807 (ttt) REVERT: A 293 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8570 (p) REVERT: A 353 GLN cc_start: 0.7187 (mm-40) cc_final: 0.6963 (tm130) REVERT: A 448 GLN cc_start: 0.7992 (pt0) cc_final: 0.7677 (pt0) REVERT: A 476 GLN cc_start: 0.7969 (mm110) cc_final: 0.7763 (mm-40) REVERT: A 486 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7686 (mp) REVERT: A 564 ARG cc_start: 0.8224 (mtt-85) cc_final: 0.8010 (mtt-85) REVERT: D 226 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7556 (m-30) REVERT: D 293 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8580 (p) REVERT: D 353 GLN cc_start: 0.7208 (mm-40) cc_final: 0.6739 (mm110) REVERT: D 448 GLN cc_start: 0.7997 (pt0) cc_final: 0.7664 (pt0) REVERT: D 486 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7741 (mp) REVERT: D 564 ARG cc_start: 0.8099 (mtt-85) cc_final: 0.7819 (mmm160) REVERT: D 615 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.7128 (mpt) REVERT: D 732 GLU cc_start: 0.6468 (tt0) cc_final: 0.6266 (tt0) REVERT: E 226 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7549 (m-30) REVERT: E 243 MET cc_start: 0.8298 (ttp) cc_final: 0.7866 (ttt) REVERT: E 285 GLN cc_start: 0.7178 (tm-30) cc_final: 0.6788 (tm130) REVERT: E 293 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8582 (p) REVERT: E 353 GLN cc_start: 0.7221 (mm-40) cc_final: 0.6732 (mm110) REVERT: E 448 GLN cc_start: 0.7964 (pt0) cc_final: 0.7661 (pt0) REVERT: E 486 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7654 (mp) REVERT: E 564 ARG cc_start: 0.8255 (mtt-85) cc_final: 0.7997 (mtt-85) REVERT: E 615 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.7140 (mpt) REVERT: F 226 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7534 (m-30) REVERT: F 243 MET cc_start: 0.8310 (ttp) cc_final: 0.7898 (ttt) REVERT: F 285 GLN cc_start: 0.7214 (tm-30) cc_final: 0.6907 (tm130) REVERT: F 293 VAL cc_start: 0.8847 (OUTLIER) cc_final: 0.8559 (p) REVERT: F 353 GLN cc_start: 0.7175 (mm-40) cc_final: 0.6740 (mm110) REVERT: F 360 LYS cc_start: 0.7328 (mmmm) cc_final: 0.7012 (tppp) REVERT: F 448 GLN cc_start: 0.7996 (pt0) cc_final: 0.7696 (pt0) REVERT: F 486 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7699 (mp) REVERT: F 564 ARG cc_start: 0.8248 (mtt-85) cc_final: 0.7982 (mtt-85) REVERT: F 615 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.7270 (mpt) outliers start: 73 outliers final: 25 residues processed: 489 average time/residue: 2.2035 time to fit residues: 1298.3925 Evaluate side-chains 486 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 446 time to evaluate : 4.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 499 GLU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 468 THR Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 486 ILE Chi-restraints excluded: chain E residue 499 GLU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 615 MET Chi-restraints excluded: chain E residue 632 ASP Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 468 THR Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 499 GLU Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 615 MET Chi-restraints excluded: chain F residue 632 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 213 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 256 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 383 ASN F 383 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 23516 Z= 0.303 Angle : 0.678 11.556 31844 Z= 0.344 Chirality : 0.107 1.544 3560 Planarity : 0.004 0.043 4064 Dihedral : 10.862 174.074 3556 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.14 % Allowed : 16.05 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 2968 helix: 0.59 (0.13), residues: 1468 sheet: -0.45 (0.22), residues: 512 loop : 0.33 (0.21), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 132 HIS 0.003 0.001 HIS E 436 PHE 0.013 0.002 PHE F 651 TYR 0.010 0.001 TYR D 385 ARG 0.010 0.001 ARG F 513 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 458 time to evaluate : 3.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7474 (pttm) cc_final: 0.7267 (pttm) REVERT: A 226 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7549 (m-30) REVERT: A 243 MET cc_start: 0.8335 (ttp) cc_final: 0.7822 (ttt) REVERT: A 293 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8534 (p) REVERT: A 365 LYS cc_start: 0.7737 (mmtm) cc_final: 0.7501 (mmmt) REVERT: A 448 GLN cc_start: 0.7977 (pt0) cc_final: 0.7740 (pt0) REVERT: A 476 GLN cc_start: 0.7938 (mm110) cc_final: 0.7736 (mm-40) REVERT: A 486 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7741 (mp) REVERT: A 564 ARG cc_start: 0.8274 (mtt-85) cc_final: 0.8012 (mtt-85) REVERT: D 226 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7550 (m-30) REVERT: D 293 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8535 (p) REVERT: D 353 GLN cc_start: 0.7272 (mm-40) cc_final: 0.6802 (mm-40) REVERT: D 440 GLU cc_start: 0.7381 (tt0) cc_final: 0.7173 (tt0) REVERT: D 448 GLN cc_start: 0.8004 (pt0) cc_final: 0.7755 (pt0) REVERT: D 486 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7785 (mp) REVERT: D 490 HIS cc_start: 0.8253 (m90) cc_final: 0.8013 (m90) REVERT: D 615 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.7137 (mpt) REVERT: D 732 GLU cc_start: 0.6466 (tt0) cc_final: 0.6255 (tt0) REVERT: E 226 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7530 (m-30) REVERT: E 243 MET cc_start: 0.8298 (ttp) cc_final: 0.7839 (ttt) REVERT: E 285 GLN cc_start: 0.7198 (tm-30) cc_final: 0.6809 (tm130) REVERT: E 293 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8537 (p) REVERT: E 353 GLN cc_start: 0.7181 (mm-40) cc_final: 0.6713 (mm110) REVERT: E 448 GLN cc_start: 0.7944 (pt0) cc_final: 0.7724 (pt0) REVERT: E 486 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7727 (mp) REVERT: E 564 ARG cc_start: 0.8253 (mtt-85) cc_final: 0.8004 (mtt-85) REVERT: E 615 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.7127 (mpt) REVERT: F 226 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7514 (m-30) REVERT: F 243 MET cc_start: 0.8280 (ttp) cc_final: 0.7839 (ttt) REVERT: F 285 GLN cc_start: 0.7216 (tm-30) cc_final: 0.6877 (tm130) REVERT: F 293 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.8522 (p) REVERT: F 353 GLN cc_start: 0.7245 (mm-40) cc_final: 0.6806 (mm110) REVERT: F 360 LYS cc_start: 0.7310 (mmmm) cc_final: 0.7012 (tppp) REVERT: F 448 GLN cc_start: 0.7972 (pt0) cc_final: 0.7756 (pt0) REVERT: F 486 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7766 (mp) REVERT: F 564 ARG cc_start: 0.8258 (mtt-85) cc_final: 0.8007 (mtt-85) REVERT: F 615 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.7184 (mpt) outliers start: 75 outliers final: 33 residues processed: 491 average time/residue: 2.3680 time to fit residues: 1412.2741 Evaluate side-chains 496 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 448 time to evaluate : 3.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 499 GLU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 652 ASP Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 322 MET Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 486 ILE Chi-restraints excluded: chain E residue 499 GLU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 615 MET Chi-restraints excluded: chain E residue 632 ASP Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 377 SER Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 499 GLU Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 615 MET Chi-restraints excluded: chain F residue 632 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 4.9990 chunk 257 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 286 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 383 ASN F 341 ASN F 383 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 23516 Z= 0.294 Angle : 0.679 11.634 31844 Z= 0.343 Chirality : 0.106 1.523 3560 Planarity : 0.004 0.039 4064 Dihedral : 10.534 174.185 3556 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.01 % Allowed : 16.93 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 2968 helix: 0.66 (0.13), residues: 1468 sheet: -0.44 (0.22), residues: 512 loop : 0.31 (0.21), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 132 HIS 0.003 0.001 HIS E 490 PHE 0.013 0.001 PHE F 651 TYR 0.010 0.001 TYR A 385 ARG 0.008 0.000 ARG E 513 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 459 time to evaluate : 3.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7540 (m-30) REVERT: A 243 MET cc_start: 0.8319 (ttp) cc_final: 0.7822 (ttt) REVERT: A 293 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8539 (p) REVERT: A 448 GLN cc_start: 0.7969 (pt0) cc_final: 0.7737 (pt0) REVERT: A 486 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7760 (mp) REVERT: A 564 ARG cc_start: 0.8285 (mtt-85) cc_final: 0.7995 (mtt-85) REVERT: D 226 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7560 (m-30) REVERT: D 293 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8533 (p) REVERT: D 353 GLN cc_start: 0.7263 (mm-40) cc_final: 0.6793 (mm-40) REVERT: D 440 GLU cc_start: 0.7317 (tt0) cc_final: 0.7088 (tt0) REVERT: D 448 GLN cc_start: 0.8004 (pt0) cc_final: 0.7758 (pt0) REVERT: D 486 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7790 (mp) REVERT: D 615 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.7154 (mpt) REVERT: D 732 GLU cc_start: 0.6466 (tt0) cc_final: 0.6249 (tt0) REVERT: E 226 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7573 (m-30) REVERT: E 243 MET cc_start: 0.8272 (ttp) cc_final: 0.7815 (ttt) REVERT: E 285 GLN cc_start: 0.7219 (tm-30) cc_final: 0.6832 (tm130) REVERT: E 293 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8534 (p) REVERT: E 353 GLN cc_start: 0.7243 (mm-40) cc_final: 0.6767 (mm110) REVERT: E 365 LYS cc_start: 0.7673 (mmtm) cc_final: 0.7377 (mmmm) REVERT: E 448 GLN cc_start: 0.7938 (pt0) cc_final: 0.7723 (pt0) REVERT: E 486 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7731 (mp) REVERT: E 564 ARG cc_start: 0.8295 (mtt-85) cc_final: 0.7967 (mtt-85) REVERT: E 615 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.7149 (mpt) REVERT: F 190 ASP cc_start: 0.8451 (m-30) cc_final: 0.8196 (m-30) REVERT: F 226 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7573 (m-30) REVERT: F 243 MET cc_start: 0.8275 (ttp) cc_final: 0.7839 (ttt) REVERT: F 285 GLN cc_start: 0.7232 (tm-30) cc_final: 0.6899 (tm130) REVERT: F 293 VAL cc_start: 0.8813 (OUTLIER) cc_final: 0.8516 (p) REVERT: F 349 MET cc_start: 0.5986 (mmm) cc_final: 0.5466 (mmm) REVERT: F 353 GLN cc_start: 0.7242 (mm-40) cc_final: 0.6783 (mm110) REVERT: F 360 LYS cc_start: 0.7263 (mmmm) cc_final: 0.6959 (tppp) REVERT: F 448 GLN cc_start: 0.7983 (pt0) cc_final: 0.7764 (pt0) REVERT: F 486 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7773 (mp) REVERT: F 564 ARG cc_start: 0.8291 (mtt-85) cc_final: 0.7934 (mtt-85) REVERT: F 615 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.7217 (mpt) outliers start: 72 outliers final: 42 residues processed: 499 average time/residue: 2.2436 time to fit residues: 1339.7724 Evaluate side-chains 511 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 454 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 499 GLU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 652 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 169 PHE Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 322 MET Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 486 ILE Chi-restraints excluded: chain E residue 499 GLU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 615 MET Chi-restraints excluded: chain E residue 632 ASP Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 169 PHE Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 377 SER Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 499 GLU Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 615 MET Chi-restraints excluded: chain F residue 632 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 285 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 383 ASN E 453 HIS F 341 ASN F 383 ASN F 453 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 23516 Z= 0.294 Angle : 0.679 11.634 31844 Z= 0.343 Chirality : 0.106 1.523 3560 Planarity : 0.004 0.039 4064 Dihedral : 10.527 174.185 3556 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.38 % Allowed : 18.27 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 2968 helix: 0.66 (0.13), residues: 1468 sheet: -0.44 (0.22), residues: 512 loop : 0.31 (0.21), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 132 HIS 0.003 0.001 HIS E 490 PHE 0.013 0.001 PHE F 651 TYR 0.010 0.001 TYR A 385 ARG 0.007 0.000 ARG E 513 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 454 time to evaluate : 3.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7540 (m-30) REVERT: A 243 MET cc_start: 0.8319 (ttp) cc_final: 0.7822 (ttt) REVERT: A 293 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8539 (p) REVERT: A 448 GLN cc_start: 0.7966 (pt0) cc_final: 0.7738 (pt0) REVERT: A 486 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7760 (mp) REVERT: A 564 ARG cc_start: 0.8283 (mtt-85) cc_final: 0.7995 (mtt-85) REVERT: D 226 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7560 (m-30) REVERT: D 293 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8534 (p) REVERT: D 353 GLN cc_start: 0.7265 (mm-40) cc_final: 0.6793 (mm-40) REVERT: D 440 GLU cc_start: 0.7314 (tt0) cc_final: 0.7088 (tt0) REVERT: D 448 GLN cc_start: 0.8001 (pt0) cc_final: 0.7758 (pt0) REVERT: D 486 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7790 (mp) REVERT: D 615 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.7154 (mpt) REVERT: D 732 GLU cc_start: 0.6469 (tt0) cc_final: 0.6249 (tt0) REVERT: E 226 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: E 243 MET cc_start: 0.8272 (ttp) cc_final: 0.7815 (ttt) REVERT: E 285 GLN cc_start: 0.7221 (tm-30) cc_final: 0.6833 (tm130) REVERT: E 293 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8534 (p) REVERT: E 353 GLN cc_start: 0.7244 (mm-40) cc_final: 0.6767 (mm110) REVERT: E 365 LYS cc_start: 0.7671 (mmtm) cc_final: 0.7378 (mmmm) REVERT: E 448 GLN cc_start: 0.7937 (pt0) cc_final: 0.7723 (pt0) REVERT: E 486 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7731 (mp) REVERT: E 564 ARG cc_start: 0.8273 (mtt-85) cc_final: 0.7968 (mtt-85) REVERT: E 615 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.7150 (mpt) REVERT: F 190 ASP cc_start: 0.8451 (m-30) cc_final: 0.8196 (m-30) REVERT: F 226 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: F 243 MET cc_start: 0.8275 (ttp) cc_final: 0.7839 (ttt) REVERT: F 285 GLN cc_start: 0.7233 (tm-30) cc_final: 0.6899 (tm130) REVERT: F 293 VAL cc_start: 0.8813 (OUTLIER) cc_final: 0.8515 (p) REVERT: F 349 MET cc_start: 0.5987 (mmm) cc_final: 0.5466 (mmm) REVERT: F 353 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6783 (mm110) REVERT: F 360 LYS cc_start: 0.7260 (mmmm) cc_final: 0.6959 (tppp) REVERT: F 448 GLN cc_start: 0.7983 (pt0) cc_final: 0.7762 (pt0) REVERT: F 486 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7774 (mp) REVERT: F 564 ARG cc_start: 0.8251 (mtt-85) cc_final: 0.7934 (mtt-85) REVERT: F 615 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.7217 (mpt) outliers start: 57 outliers final: 42 residues processed: 487 average time/residue: 2.2628 time to fit residues: 1327.2903 Evaluate side-chains 509 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 452 time to evaluate : 3.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 499 GLU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 652 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 169 PHE Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 322 MET Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 486 ILE Chi-restraints excluded: chain E residue 499 GLU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 615 MET Chi-restraints excluded: chain E residue 632 ASP Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 169 PHE Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 377 SER Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 499 GLU Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 615 MET Chi-restraints excluded: chain F residue 632 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 170 optimal weight: 0.0370 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 383 ASN E 453 HIS F 341 ASN F 383 ASN F 453 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 23516 Z= 0.294 Angle : 0.679 11.634 31844 Z= 0.343 Chirality : 0.106 1.523 3560 Planarity : 0.004 0.039 4064 Dihedral : 10.526 174.185 3556 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.38 % Allowed : 18.27 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 2968 helix: 0.66 (0.13), residues: 1468 sheet: -0.44 (0.22), residues: 512 loop : 0.31 (0.21), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 132 HIS 0.003 0.001 HIS E 490 PHE 0.013 0.001 PHE F 651 TYR 0.010 0.001 TYR A 385 ARG 0.007 0.000 ARG E 513 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 452 time to evaluate : 3.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7540 (m-30) REVERT: A 243 MET cc_start: 0.8319 (ttp) cc_final: 0.7822 (ttt) REVERT: A 293 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8539 (p) REVERT: A 448 GLN cc_start: 0.7966 (pt0) cc_final: 0.7738 (pt0) REVERT: A 486 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7760 (mp) REVERT: A 564 ARG cc_start: 0.8283 (mtt-85) cc_final: 0.7995 (mtt-85) REVERT: D 226 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7560 (m-30) REVERT: D 293 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8534 (p) REVERT: D 353 GLN cc_start: 0.7264 (mm-40) cc_final: 0.6793 (mm-40) REVERT: D 440 GLU cc_start: 0.7314 (tt0) cc_final: 0.7088 (tt0) REVERT: D 448 GLN cc_start: 0.8001 (pt0) cc_final: 0.7758 (pt0) REVERT: D 486 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7790 (mp) REVERT: D 615 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.7154 (mpt) REVERT: D 732 GLU cc_start: 0.6469 (tt0) cc_final: 0.6249 (tt0) REVERT: E 226 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: E 243 MET cc_start: 0.8272 (ttp) cc_final: 0.7815 (ttt) REVERT: E 285 GLN cc_start: 0.7221 (tm-30) cc_final: 0.6833 (tm130) REVERT: E 293 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8534 (p) REVERT: E 353 GLN cc_start: 0.7244 (mm-40) cc_final: 0.6767 (mm110) REVERT: E 365 LYS cc_start: 0.7671 (mmtm) cc_final: 0.7378 (mmmm) REVERT: E 448 GLN cc_start: 0.7936 (pt0) cc_final: 0.7723 (pt0) REVERT: E 486 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7731 (mp) REVERT: E 564 ARG cc_start: 0.8274 (mtt-85) cc_final: 0.7968 (mtt-85) REVERT: E 615 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.7150 (mpt) REVERT: F 190 ASP cc_start: 0.8450 (m-30) cc_final: 0.8195 (m-30) REVERT: F 226 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: F 243 MET cc_start: 0.8275 (ttp) cc_final: 0.7839 (ttt) REVERT: F 285 GLN cc_start: 0.7234 (tm-30) cc_final: 0.6899 (tm130) REVERT: F 293 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8515 (p) REVERT: F 349 MET cc_start: 0.5987 (mmm) cc_final: 0.5466 (mmm) REVERT: F 353 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6783 (mm110) REVERT: F 360 LYS cc_start: 0.7260 (mmmm) cc_final: 0.6959 (tppp) REVERT: F 448 GLN cc_start: 0.7980 (pt0) cc_final: 0.7762 (pt0) REVERT: F 486 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7773 (mp) REVERT: F 564 ARG cc_start: 0.8251 (mtt-85) cc_final: 0.7934 (mtt-85) REVERT: F 615 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.7217 (mpt) outliers start: 57 outliers final: 42 residues processed: 485 average time/residue: 2.2597 time to fit residues: 1311.6180 Evaluate side-chains 509 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 452 time to evaluate : 3.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 499 GLU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 652 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 169 PHE Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 322 MET Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 486 ILE Chi-restraints excluded: chain E residue 499 GLU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 615 MET Chi-restraints excluded: chain E residue 632 ASP Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 169 PHE Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 377 SER Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 499 GLU Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 615 MET Chi-restraints excluded: chain F residue 632 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 2.9990 chunk 273 optimal weight: 0.6980 chunk 249 optimal weight: 1.9990 chunk 265 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 240 optimal weight: 2.9990 chunk 251 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 383 ASN E 453 HIS F 341 ASN F 383 ASN F 453 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 23516 Z= 0.294 Angle : 0.679 11.634 31844 Z= 0.343 Chirality : 0.106 1.523 3560 Planarity : 0.004 0.039 4064 Dihedral : 10.526 174.185 3556 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.38 % Allowed : 18.23 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 2968 helix: 0.66 (0.13), residues: 1468 sheet: -0.44 (0.22), residues: 512 loop : 0.31 (0.21), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 132 HIS 0.003 0.001 HIS E 490 PHE 0.013 0.001 PHE F 651 TYR 0.010 0.001 TYR A 385 ARG 0.007 0.000 ARG E 513 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 452 time to evaluate : 3.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7540 (m-30) REVERT: A 243 MET cc_start: 0.8319 (ttp) cc_final: 0.7822 (ttt) REVERT: A 293 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8539 (p) REVERT: A 448 GLN cc_start: 0.7967 (pt0) cc_final: 0.7738 (pt0) REVERT: A 486 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7760 (mp) REVERT: A 564 ARG cc_start: 0.8283 (mtt-85) cc_final: 0.7995 (mtt-85) REVERT: D 226 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7560 (m-30) REVERT: D 293 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8534 (p) REVERT: D 353 GLN cc_start: 0.7264 (mm-40) cc_final: 0.6793 (mm-40) REVERT: D 440 GLU cc_start: 0.7314 (tt0) cc_final: 0.7088 (tt0) REVERT: D 448 GLN cc_start: 0.8001 (pt0) cc_final: 0.7758 (pt0) REVERT: D 486 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7790 (mp) REVERT: D 615 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.7154 (mpt) REVERT: D 732 GLU cc_start: 0.6469 (tt0) cc_final: 0.6249 (tt0) REVERT: E 226 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: E 243 MET cc_start: 0.8272 (ttp) cc_final: 0.7815 (ttt) REVERT: E 285 GLN cc_start: 0.7221 (tm-30) cc_final: 0.6833 (tm130) REVERT: E 293 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8534 (p) REVERT: E 353 GLN cc_start: 0.7244 (mm-40) cc_final: 0.6767 (mm110) REVERT: E 365 LYS cc_start: 0.7671 (mmtm) cc_final: 0.7378 (mmmm) REVERT: E 448 GLN cc_start: 0.7936 (pt0) cc_final: 0.7723 (pt0) REVERT: E 486 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7731 (mp) REVERT: E 564 ARG cc_start: 0.8274 (mtt-85) cc_final: 0.7968 (mtt-85) REVERT: E 615 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.7150 (mpt) REVERT: F 190 ASP cc_start: 0.8450 (m-30) cc_final: 0.8196 (m-30) REVERT: F 226 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: F 243 MET cc_start: 0.8275 (ttp) cc_final: 0.7839 (ttt) REVERT: F 285 GLN cc_start: 0.7234 (tm-30) cc_final: 0.6899 (tm130) REVERT: F 293 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8515 (p) REVERT: F 349 MET cc_start: 0.5987 (mmm) cc_final: 0.5466 (mmm) REVERT: F 353 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6783 (mm110) REVERT: F 360 LYS cc_start: 0.7260 (mmmm) cc_final: 0.6959 (tppp) REVERT: F 448 GLN cc_start: 0.7980 (pt0) cc_final: 0.7762 (pt0) REVERT: F 486 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7774 (mp) REVERT: F 564 ARG cc_start: 0.8251 (mtt-85) cc_final: 0.7934 (mtt-85) REVERT: F 615 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.7217 (mpt) outliers start: 57 outliers final: 42 residues processed: 485 average time/residue: 2.2685 time to fit residues: 1320.0703 Evaluate side-chains 509 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 452 time to evaluate : 3.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 499 GLU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 652 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 169 PHE Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 322 MET Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 486 ILE Chi-restraints excluded: chain E residue 499 GLU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 615 MET Chi-restraints excluded: chain E residue 632 ASP Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 169 PHE Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 377 SER Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 499 GLU Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 615 MET Chi-restraints excluded: chain F residue 632 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 0.0070 chunk 281 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 195 optimal weight: 0.6980 chunk 294 optimal weight: 0.9990 chunk 271 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 overall best weight: 1.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 383 ASN E 453 HIS F 341 ASN F 383 ASN F 453 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 23516 Z= 0.294 Angle : 0.679 11.634 31844 Z= 0.343 Chirality : 0.106 1.523 3560 Planarity : 0.004 0.039 4064 Dihedral : 10.526 174.185 3556 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.38 % Allowed : 18.27 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 2968 helix: 0.66 (0.13), residues: 1468 sheet: -0.44 (0.22), residues: 512 loop : 0.31 (0.21), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 132 HIS 0.003 0.001 HIS E 490 PHE 0.013 0.001 PHE F 651 TYR 0.010 0.001 TYR A 385 ARG 0.007 0.000 ARG E 513 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 452 time to evaluate : 4.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7540 (m-30) REVERT: A 243 MET cc_start: 0.8319 (ttp) cc_final: 0.7822 (ttt) REVERT: A 293 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8539 (p) REVERT: A 448 GLN cc_start: 0.7966 (pt0) cc_final: 0.7738 (pt0) REVERT: A 486 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7760 (mp) REVERT: A 564 ARG cc_start: 0.8283 (mtt-85) cc_final: 0.7995 (mtt-85) REVERT: D 226 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7560 (m-30) REVERT: D 293 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8534 (p) REVERT: D 353 GLN cc_start: 0.7264 (mm-40) cc_final: 0.6793 (mm-40) REVERT: D 440 GLU cc_start: 0.7314 (tt0) cc_final: 0.7088 (tt0) REVERT: D 448 GLN cc_start: 0.8001 (pt0) cc_final: 0.7758 (pt0) REVERT: D 486 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7790 (mp) REVERT: D 615 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.7154 (mpt) REVERT: D 732 GLU cc_start: 0.6469 (tt0) cc_final: 0.6249 (tt0) REVERT: E 226 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: E 243 MET cc_start: 0.8272 (ttp) cc_final: 0.7815 (ttt) REVERT: E 285 GLN cc_start: 0.7221 (tm-30) cc_final: 0.6833 (tm130) REVERT: E 293 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8534 (p) REVERT: E 353 GLN cc_start: 0.7244 (mm-40) cc_final: 0.6767 (mm110) REVERT: E 365 LYS cc_start: 0.7671 (mmtm) cc_final: 0.7378 (mmmm) REVERT: E 448 GLN cc_start: 0.7936 (pt0) cc_final: 0.7723 (pt0) REVERT: E 486 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7731 (mp) REVERT: E 564 ARG cc_start: 0.8274 (mtt-85) cc_final: 0.7968 (mtt-85) REVERT: E 615 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.7150 (mpt) REVERT: F 190 ASP cc_start: 0.8450 (m-30) cc_final: 0.8195 (m-30) REVERT: F 226 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: F 243 MET cc_start: 0.8275 (ttp) cc_final: 0.7839 (ttt) REVERT: F 285 GLN cc_start: 0.7234 (tm-30) cc_final: 0.6899 (tm130) REVERT: F 293 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8515 (p) REVERT: F 349 MET cc_start: 0.5987 (mmm) cc_final: 0.5466 (mmm) REVERT: F 353 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6783 (mm110) REVERT: F 360 LYS cc_start: 0.7260 (mmmm) cc_final: 0.6959 (tppp) REVERT: F 448 GLN cc_start: 0.7980 (pt0) cc_final: 0.7762 (pt0) REVERT: F 486 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7773 (mp) REVERT: F 564 ARG cc_start: 0.8251 (mtt-85) cc_final: 0.7934 (mtt-85) REVERT: F 615 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.7217 (mpt) outliers start: 57 outliers final: 42 residues processed: 485 average time/residue: 2.1975 time to fit residues: 1274.1103 Evaluate side-chains 509 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 452 time to evaluate : 3.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 499 GLU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 652 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 169 PHE Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 322 MET Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 486 ILE Chi-restraints excluded: chain E residue 499 GLU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 615 MET Chi-restraints excluded: chain E residue 632 ASP Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 169 PHE Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 377 SER Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 499 GLU Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 615 MET Chi-restraints excluded: chain F residue 632 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 0.4980 chunk 250 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 383 ASN E 453 HIS F 341 ASN F 383 ASN F 453 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.149661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.120114 restraints weight = 74663.740| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.66 r_work: 0.3149 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 23516 Z= 0.294 Angle : 0.679 11.634 31844 Z= 0.343 Chirality : 0.106 1.523 3560 Planarity : 0.004 0.039 4064 Dihedral : 10.526 174.185 3556 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.38 % Allowed : 18.23 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 2968 helix: 0.66 (0.13), residues: 1468 sheet: -0.44 (0.22), residues: 512 loop : 0.31 (0.21), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 132 HIS 0.003 0.001 HIS E 490 PHE 0.013 0.001 PHE F 651 TYR 0.010 0.001 TYR A 385 ARG 0.007 0.000 ARG E 513 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19205.76 seconds wall clock time: 336 minutes 39.91 seconds (20199.91 seconds total)