Starting phenix.real_space_refine on Tue Mar 19 05:05:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vda_31912/03_2024/7vda_31912.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vda_31912/03_2024/7vda_31912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vda_31912/03_2024/7vda_31912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vda_31912/03_2024/7vda_31912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vda_31912/03_2024/7vda_31912.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vda_31912/03_2024/7vda_31912.pdb" } resolution = 2.26 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 14736 2.51 5 N 4074 2.21 5 O 4368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 102": "OD1" <-> "OD2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "B PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 102": "OD1" <-> "OD2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 318": "OD1" <-> "OD2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "C PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 102": "OD1" <-> "OD2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 318": "OD1" <-> "OD2" Residue "C GLU 402": "OE1" <-> "OE2" Residue "D PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 102": "OD1" <-> "OD2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 318": "OD1" <-> "OD2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "E PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 102": "OD1" <-> "OD2" Residue "E GLU 173": "OE1" <-> "OE2" Residue "E TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 318": "OD1" <-> "OD2" Residue "E GLU 402": "OE1" <-> "OE2" Residue "F PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 102": "OD1" <-> "OD2" Residue "F GLU 173": "OE1" <-> "OE2" Residue "F TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 318": "OD1" <-> "OD2" Residue "F GLU 402": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23292 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3882 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "B" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3882 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "C" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3882 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "D" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3882 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "E" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3882 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "F" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3882 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Time building chain proxies: 11.39, per 1000 atoms: 0.49 Number of scatterers: 23292 At special positions: 0 Unit cell: (109.85, 117.65, 156.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4368 8.00 N 4074 7.00 C 14736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 8.58 Conformation dependent library (CDL) restraints added in 4.3 seconds 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5400 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 9 sheets defined 58.5% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 8 through 31 removed outlier: 4.853A pdb=" N ASP A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LYS A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 53 Processing helix chain 'A' and resid 100 through 118 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 137 through 155 removed outlier: 3.530A pdb=" N LYS A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 186 Processing helix chain 'A' and resid 193 through 198 removed outlier: 4.115A pdb=" N VAL A 198 " --> pdb=" O HIS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 213 through 228 removed outlier: 3.666A pdb=" N PHE A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.979A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 removed outlier: 3.572A pdb=" N PHE A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 299 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.946A pdb=" N VAL A 317 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.605A pdb=" N VAL A 339 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'A' and resid 375 through 391 Processing helix chain 'A' and resid 398 through 421 Processing helix chain 'A' and resid 433 through 442 Processing helix chain 'A' and resid 444 through 471 removed outlier: 3.739A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 497 removed outlier: 3.589A pdb=" N ALA A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 31 removed outlier: 4.853A pdb=" N ASP B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 53 Processing helix chain 'B' and resid 100 through 118 Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 137 through 155 removed outlier: 3.529A pdb=" N LYS B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 186 Processing helix chain 'B' and resid 193 through 198 removed outlier: 4.115A pdb=" N VAL B 198 " --> pdb=" O HIS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.666A pdb=" N PHE B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 237 removed outlier: 3.980A pdb=" N ILE B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 removed outlier: 3.572A pdb=" N PHE B 266 " --> pdb=" O TYR B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 299 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.947A pdb=" N VAL B 317 " --> pdb=" O ILE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.607A pdb=" N VAL B 339 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'B' and resid 375 through 391 Processing helix chain 'B' and resid 398 through 421 Processing helix chain 'B' and resid 433 through 442 Processing helix chain 'B' and resid 444 through 471 removed outlier: 3.739A pdb=" N ILE B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 497 removed outlier: 3.589A pdb=" N ALA B 480 " --> pdb=" O ASP B 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 31 removed outlier: 4.852A pdb=" N ASP C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 53 Processing helix chain 'C' and resid 100 through 118 Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 137 through 155 removed outlier: 3.530A pdb=" N LYS C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 186 Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.114A pdb=" N VAL C 198 " --> pdb=" O HIS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 213 through 228 removed outlier: 3.665A pdb=" N PHE C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 237 removed outlier: 3.980A pdb=" N ILE C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 266 removed outlier: 3.572A pdb=" N PHE C 266 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 299 Processing helix chain 'C' and resid 313 through 317 removed outlier: 3.947A pdb=" N VAL C 317 " --> pdb=" O ILE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.606A pdb=" N VAL C 339 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'C' and resid 375 through 391 Processing helix chain 'C' and resid 398 through 421 Processing helix chain 'C' and resid 433 through 442 Processing helix chain 'C' and resid 444 through 471 removed outlier: 3.740A pdb=" N ILE C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 497 removed outlier: 3.589A pdb=" N ALA C 480 " --> pdb=" O ASP C 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 31 removed outlier: 4.853A pdb=" N ASP D 26 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 53 Processing helix chain 'D' and resid 100 through 118 Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 137 through 155 removed outlier: 3.529A pdb=" N LYS D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 186 Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.115A pdb=" N VAL D 198 " --> pdb=" O HIS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 213 through 228 removed outlier: 3.665A pdb=" N PHE D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 237 removed outlier: 3.979A pdb=" N ILE D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 266 removed outlier: 3.573A pdb=" N PHE D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 299 Processing helix chain 'D' and resid 313 through 317 removed outlier: 3.946A pdb=" N VAL D 317 " --> pdb=" O ILE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.606A pdb=" N VAL D 339 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 363 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'D' and resid 375 through 391 Processing helix chain 'D' and resid 398 through 421 Processing helix chain 'D' and resid 433 through 442 Processing helix chain 'D' and resid 444 through 471 removed outlier: 3.739A pdb=" N ILE D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 497 removed outlier: 3.589A pdb=" N ALA D 480 " --> pdb=" O ASP D 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 31 removed outlier: 4.853A pdb=" N ASP E 26 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS E 27 " --> pdb=" O ILE E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 53 Processing helix chain 'E' and resid 100 through 118 Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 137 through 155 removed outlier: 3.530A pdb=" N LYS E 155 " --> pdb=" O GLU E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 186 Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.114A pdb=" N VAL E 198 " --> pdb=" O HIS E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 213 through 228 removed outlier: 3.666A pdb=" N PHE E 226 " --> pdb=" O GLY E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 237 removed outlier: 3.979A pdb=" N ILE E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 266 removed outlier: 3.572A pdb=" N PHE E 266 " --> pdb=" O TYR E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 299 Processing helix chain 'E' and resid 313 through 317 removed outlier: 3.946A pdb=" N VAL E 317 " --> pdb=" O ILE E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 339 removed outlier: 3.606A pdb=" N VAL E 339 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 363 Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'E' and resid 375 through 391 Processing helix chain 'E' and resid 398 through 421 Processing helix chain 'E' and resid 433 through 442 Processing helix chain 'E' and resid 444 through 471 removed outlier: 3.739A pdb=" N ILE E 448 " --> pdb=" O SER E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 497 removed outlier: 3.589A pdb=" N ALA E 480 " --> pdb=" O ASP E 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 31 removed outlier: 4.853A pdb=" N ASP F 26 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 53 Processing helix chain 'F' and resid 100 through 118 Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 137 through 155 removed outlier: 3.530A pdb=" N LYS F 155 " --> pdb=" O GLU F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 186 Processing helix chain 'F' and resid 193 through 198 removed outlier: 4.114A pdb=" N VAL F 198 " --> pdb=" O HIS F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 213 through 228 removed outlier: 3.665A pdb=" N PHE F 226 " --> pdb=" O GLY F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 237 removed outlier: 3.980A pdb=" N ILE F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 266 removed outlier: 3.573A pdb=" N PHE F 266 " --> pdb=" O TYR F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 299 Processing helix chain 'F' and resid 313 through 317 removed outlier: 3.946A pdb=" N VAL F 317 " --> pdb=" O ILE F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 339 removed outlier: 3.606A pdb=" N VAL F 339 " --> pdb=" O ALA F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 363 Processing helix chain 'F' and resid 369 through 374 Processing helix chain 'F' and resid 375 through 391 Processing helix chain 'F' and resid 398 through 421 Processing helix chain 'F' and resid 433 through 442 Processing helix chain 'F' and resid 444 through 471 removed outlier: 3.740A pdb=" N ILE F 448 " --> pdb=" O SER F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 497 removed outlier: 3.589A pdb=" N ALA F 480 " --> pdb=" O ASP F 476 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 163 through 166 removed outlier: 6.547A pdb=" N CYS A 89 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ALA A 166 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY A 91 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY A 92 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY E 92 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS E 89 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ALA E 166 " --> pdb=" O CYS E 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY E 91 " --> pdb=" O ALA E 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 308 through 309 removed outlier: 3.670A pdb=" N GLY A 278 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 273 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE A 247 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N GLY A 274 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A 249 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU A 322 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE A 344 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 163 through 166 removed outlier: 6.548A pdb=" N CYS B 89 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ALA B 166 " --> pdb=" O CYS B 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY B 91 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY B 92 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY D 92 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS D 89 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ALA D 166 " --> pdb=" O CYS D 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY D 91 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 308 through 309 removed outlier: 3.669A pdb=" N GLY B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 273 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE B 247 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N GLY B 274 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 249 " --> pdb=" O GLY B 274 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 322 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE B 344 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 163 through 166 removed outlier: 6.548A pdb=" N CYS C 89 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ALA C 166 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY C 91 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY C 92 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY F 92 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS F 89 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ALA F 166 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY F 91 " --> pdb=" O ALA F 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 308 through 309 removed outlier: 3.669A pdb=" N GLY C 278 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL C 273 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE C 247 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N GLY C 274 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL C 249 " --> pdb=" O GLY C 274 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU C 322 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE C 344 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 308 through 309 removed outlier: 3.669A pdb=" N GLY D 278 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 273 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE D 247 " --> pdb=" O THR D 272 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N GLY D 274 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL D 249 " --> pdb=" O GLY D 274 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU D 322 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE D 344 " --> pdb=" O ILE D 368 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 308 through 309 removed outlier: 3.669A pdb=" N GLY E 278 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL E 273 " --> pdb=" O ILE E 280 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE E 247 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N GLY E 274 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL E 249 " --> pdb=" O GLY E 274 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU E 322 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE E 344 " --> pdb=" O ILE E 368 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 308 through 309 removed outlier: 3.669A pdb=" N GLY F 278 " --> pdb=" O GLU F 275 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL F 273 " --> pdb=" O ILE F 280 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE F 247 " --> pdb=" O THR F 272 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N GLY F 274 " --> pdb=" O PHE F 247 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL F 249 " --> pdb=" O GLY F 274 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU F 322 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE F 344 " --> pdb=" O ILE F 368 " (cutoff:3.500A) 1374 hydrogen bonds defined for protein. 3924 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: 7.93 Time building geometry restraints manager: 9.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7746 1.35 - 1.46: 5388 1.46 - 1.58: 10464 1.58 - 1.70: 0 1.70 - 1.82: 192 Bond restraints: 23790 Sorted by residual: bond pdb=" CB LYS A 342 " pdb=" CG LYS A 342 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.25e+00 bond pdb=" CB LYS B 342 " pdb=" CG LYS B 342 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.24e+00 bond pdb=" CB LYS C 342 " pdb=" CG LYS C 342 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CB LYS D 342 " pdb=" CG LYS D 342 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CB LYS F 342 " pdb=" CG LYS F 342 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 ... (remaining 23785 not shown) Histogram of bond angle deviations from ideal: 98.49 - 105.59: 438 105.59 - 112.68: 12441 112.68 - 119.78: 7761 119.78 - 126.88: 11220 126.88 - 133.97: 258 Bond angle restraints: 32118 Sorted by residual: angle pdb=" CB MET E 233 " pdb=" CG MET E 233 " pdb=" SD MET E 233 " ideal model delta sigma weight residual 112.70 122.75 -10.05 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CB MET A 233 " pdb=" CG MET A 233 " pdb=" SD MET A 233 " ideal model delta sigma weight residual 112.70 122.75 -10.05 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CB MET B 233 " pdb=" CG MET B 233 " pdb=" SD MET B 233 " ideal model delta sigma weight residual 112.70 122.72 -10.02 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CB MET C 233 " pdb=" CG MET C 233 " pdb=" SD MET C 233 " ideal model delta sigma weight residual 112.70 122.72 -10.02 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CB MET F 233 " pdb=" CG MET F 233 " pdb=" SD MET F 233 " ideal model delta sigma weight residual 112.70 122.72 -10.02 3.00e+00 1.11e-01 1.11e+01 ... (remaining 32113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 12196 17.78 - 35.55: 1460 35.55 - 53.33: 468 53.33 - 71.11: 90 71.11 - 88.88: 48 Dihedral angle restraints: 14262 sinusoidal: 5784 harmonic: 8478 Sorted by residual: dihedral pdb=" CA LYS D 420 " pdb=" C LYS D 420 " pdb=" N PHE D 421 " pdb=" CA PHE D 421 " ideal model delta harmonic sigma weight residual 180.00 157.84 22.16 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA LYS B 420 " pdb=" C LYS B 420 " pdb=" N PHE B 421 " pdb=" CA PHE B 421 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA LYS E 420 " pdb=" C LYS E 420 " pdb=" N PHE E 421 " pdb=" CA PHE E 421 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 14259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2138 0.028 - 0.056: 821 0.056 - 0.084: 311 0.084 - 0.111: 157 0.111 - 0.139: 65 Chirality restraints: 3492 Sorted by residual: chirality pdb=" CA ILE D 280 " pdb=" N ILE D 280 " pdb=" C ILE D 280 " pdb=" CB ILE D 280 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE B 280 " pdb=" N ILE B 280 " pdb=" C ILE B 280 " pdb=" CB ILE B 280 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE C 280 " pdb=" N ILE C 280 " pdb=" C ILE C 280 " pdb=" CB ILE C 280 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 3489 not shown) Planarity restraints: 4182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 282 " -0.035 5.00e-02 4.00e+02 5.42e-02 4.71e+00 pdb=" N PRO D 283 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 283 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 283 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 282 " 0.035 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO A 283 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 282 " 0.035 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO B 283 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 283 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 283 " 0.030 5.00e-02 4.00e+02 ... (remaining 4179 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 425 2.69 - 3.25: 22597 3.25 - 3.80: 38986 3.80 - 4.35: 51149 4.35 - 4.90: 85292 Nonbonded interactions: 198449 Sorted by model distance: nonbonded pdb=" OG1 THR F 272 " pdb=" O ILE F 280 " model vdw 2.142 2.440 nonbonded pdb=" OG1 THR A 272 " pdb=" O ILE A 280 " model vdw 2.143 2.440 nonbonded pdb=" OG1 THR B 272 " pdb=" O ILE B 280 " model vdw 2.143 2.440 nonbonded pdb=" OG1 THR E 272 " pdb=" O ILE E 280 " model vdw 2.143 2.440 nonbonded pdb=" OG1 THR C 272 " pdb=" O ILE C 280 " model vdw 2.143 2.440 ... (remaining 198444 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 'B' selection = chain 'C' 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.430 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 59.460 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.130 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23790 Z= 0.166 Angle : 0.531 10.055 32118 Z= 0.296 Chirality : 0.041 0.139 3492 Planarity : 0.004 0.054 4182 Dihedral : 17.671 88.884 8862 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.20 % Allowed : 19.15 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.67 (0.16), residues: 2964 helix: 2.57 (0.13), residues: 1542 sheet: -0.25 (0.28), residues: 396 loop : -0.63 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 281 HIS 0.004 0.001 HIS D 258 PHE 0.028 0.001 PHE B 360 TYR 0.012 0.001 TYR B 407 ARG 0.003 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 323 time to evaluate : 2.760 Fit side-chains REVERT: A 269 LYS cc_start: 0.7252 (OUTLIER) cc_final: 0.6771 (ptmm) REVERT: A 342 LYS cc_start: 0.5378 (mmpt) cc_final: 0.4841 (mppt) REVERT: B 233 MET cc_start: 0.6251 (mmp) cc_final: 0.5806 (mmm) REVERT: C 11 LYS cc_start: 0.7198 (mmmt) cc_final: 0.6939 (mppt) REVERT: D 340 LYS cc_start: 0.5513 (mmtp) cc_final: 0.5149 (pttt) REVERT: D 342 LYS cc_start: 0.5476 (mmpt) cc_final: 0.4933 (mppt) REVERT: F 11 LYS cc_start: 0.7207 (mmmt) cc_final: 0.6941 (mppt) outliers start: 55 outliers final: 48 residues processed: 362 average time/residue: 1.5177 time to fit residues: 620.8950 Evaluate side-chains 341 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 292 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 397 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 6.9990 chunk 222 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 230 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 266 optimal weight: 8.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN A 463 GLN ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN C 374 ASN C 463 GLN ** D 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN D 463 GLN ** E 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 ASN F 374 ASN F 463 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 23790 Z= 0.321 Angle : 0.640 7.440 32118 Z= 0.344 Chirality : 0.048 0.146 3492 Planarity : 0.006 0.060 4182 Dihedral : 7.300 55.144 3337 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 7.25 % Allowed : 15.38 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.90 (0.15), residues: 2964 helix: 1.88 (0.13), residues: 1584 sheet: -0.40 (0.26), residues: 396 loop : -1.11 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP E 281 HIS 0.007 0.002 HIS A 85 PHE 0.031 0.003 PHE F 360 TYR 0.013 0.002 TYR D 190 ARG 0.005 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 313 time to evaluate : 2.593 Fit side-chains REVERT: A 25 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6366 (tt0) REVERT: A 269 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6817 (ptpp) REVERT: A 342 LYS cc_start: 0.5540 (mmpt) cc_final: 0.5047 (mmtt) REVERT: A 357 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.7042 (m-30) REVERT: B 44 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6551 (ttt-90) REVERT: B 269 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6972 (ptpp) REVERT: B 402 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7094 (pt0) REVERT: C 11 LYS cc_start: 0.7324 (mmmt) cc_final: 0.7008 (mppt) REVERT: C 25 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6334 (tt0) REVERT: C 224 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7239 (pt0) REVERT: C 269 LYS cc_start: 0.7187 (OUTLIER) cc_final: 0.6940 (ptpp) REVERT: C 281 TRP cc_start: 0.5707 (t60) cc_final: 0.5427 (t60) REVERT: C 342 LYS cc_start: 0.5571 (mmpt) cc_final: 0.5012 (mppt) REVERT: D 25 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6386 (tt0) REVERT: D 269 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6813 (ptpp) REVERT: D 342 LYS cc_start: 0.5517 (mmpt) cc_final: 0.4991 (mmtt) REVERT: D 357 ASP cc_start: 0.7229 (OUTLIER) cc_final: 0.6983 (m-30) REVERT: E 44 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6720 (ttt-90) REVERT: E 269 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6994 (ptpp) REVERT: E 402 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7106 (pt0) REVERT: F 11 LYS cc_start: 0.7326 (mmmt) cc_final: 0.7010 (mppt) REVERT: F 25 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.6335 (tt0) REVERT: F 224 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7236 (pt0) REVERT: F 269 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6927 (ptpp) REVERT: F 342 LYS cc_start: 0.5550 (mmpt) cc_final: 0.4767 (mttp) outliers start: 181 outliers final: 82 residues processed: 439 average time/residue: 1.3548 time to fit residues: 679.7531 Evaluate side-chains 405 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 305 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 269 LYS Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 357 ASP Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 430 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 222 optimal weight: 0.9990 chunk 181 optimal weight: 9.9990 chunk 73 optimal weight: 0.2980 chunk 267 optimal weight: 5.9990 chunk 288 optimal weight: 5.9990 chunk 238 optimal weight: 0.2980 chunk 265 optimal weight: 6.9990 chunk 91 optimal weight: 0.0060 chunk 214 optimal weight: 8.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 330 GLN A 414 GLN A 463 GLN B 254 ASN B 374 ASN B 414 GLN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN C 330 GLN D 254 ASN D 414 GLN D 463 GLN E 254 ASN E 374 ASN E 414 GLN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 23790 Z= 0.139 Angle : 0.472 6.518 32118 Z= 0.255 Chirality : 0.042 0.126 3492 Planarity : 0.004 0.039 4182 Dihedral : 5.851 49.741 3337 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.17 % Allowed : 17.95 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.35 (0.16), residues: 2964 helix: 2.39 (0.13), residues: 1584 sheet: -0.47 (0.26), residues: 396 loop : -1.05 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 385 HIS 0.012 0.001 HIS B 264 PHE 0.025 0.001 PHE C 360 TYR 0.011 0.001 TYR D 407 ARG 0.002 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 308 time to evaluate : 2.633 Fit side-chains REVERT: A 342 LYS cc_start: 0.5361 (mmpt) cc_final: 0.4987 (mppt) REVERT: B 269 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6823 (ptpp) REVERT: C 11 LYS cc_start: 0.7265 (mmmt) cc_final: 0.6992 (mppt) REVERT: C 25 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6220 (tt0) REVERT: C 72 TRP cc_start: 0.7267 (m100) cc_final: 0.6955 (m100) REVERT: C 224 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7176 (pt0) REVERT: C 264 HIS cc_start: 0.7306 (t-170) cc_final: 0.7096 (t70) REVERT: C 269 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6808 (ptpp) REVERT: D 25 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6316 (tt0) REVERT: F 11 LYS cc_start: 0.7257 (mmmt) cc_final: 0.6984 (mppt) REVERT: F 25 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6217 (tt0) REVERT: F 72 TRP cc_start: 0.7261 (m100) cc_final: 0.6956 (m100) REVERT: F 224 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7179 (pt0) REVERT: F 269 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6799 (ptpp) outliers start: 129 outliers final: 45 residues processed: 381 average time/residue: 1.4603 time to fit residues: 630.3668 Evaluate side-chains 356 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 303 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 430 ILE Chi-restraints excluded: chain F residue 501 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 10.0000 chunk 201 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 chunk 268 optimal weight: 20.0000 chunk 284 optimal weight: 8.9990 chunk 140 optimal weight: 0.0770 chunk 254 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 overall best weight: 6.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 374 ASN A 463 GLN B 254 ASN B 297 GLN B 463 GLN C 254 ASN C 374 ASN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN D 374 ASN D 463 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 ASN E 297 GLN E 463 GLN F 254 ASN F 374 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 23790 Z= 0.412 Angle : 0.701 8.322 32118 Z= 0.379 Chirality : 0.051 0.160 3492 Planarity : 0.007 0.084 4182 Dihedral : 6.702 55.647 3302 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 6.93 % Allowed : 17.19 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.59 (0.15), residues: 2964 helix: 1.69 (0.13), residues: 1584 sheet: -0.30 (0.27), residues: 396 loop : -1.50 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP A 281 HIS 0.008 0.002 HIS E 189 PHE 0.032 0.003 PHE C 360 TYR 0.017 0.003 TYR D 190 ARG 0.005 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 329 time to evaluate : 2.798 Fit side-chains REVERT: A 25 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6321 (tt0) REVERT: A 110 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8692 (tm) REVERT: A 292 GLU cc_start: 0.6188 (OUTLIER) cc_final: 0.5888 (tt0) REVERT: A 342 LYS cc_start: 0.5600 (mmpt) cc_final: 0.5279 (mmtm) REVERT: A 357 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.6996 (m-30) REVERT: B 44 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6791 (ttt-90) REVERT: B 269 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6956 (ptpp) REVERT: B 402 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7122 (pt0) REVERT: C 11 LYS cc_start: 0.7338 (mmmt) cc_final: 0.7038 (mppt) REVERT: C 224 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7236 (pt0) REVERT: C 227 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7369 (mm) REVERT: C 269 LYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6926 (ptpp) REVERT: C 281 TRP cc_start: 0.5818 (t60) cc_final: 0.5597 (t60) REVERT: C 292 GLU cc_start: 0.6006 (OUTLIER) cc_final: 0.5768 (tt0) REVERT: C 342 LYS cc_start: 0.5634 (mmpt) cc_final: 0.4753 (mttp) REVERT: D 25 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6308 (tt0) REVERT: D 110 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8694 (tm) REVERT: D 292 GLU cc_start: 0.6189 (OUTLIER) cc_final: 0.5891 (tt0) REVERT: D 342 LYS cc_start: 0.5610 (mmpt) cc_final: 0.5236 (mmtt) REVERT: D 357 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.7009 (m-30) REVERT: E 44 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6780 (ttt-90) REVERT: E 292 GLU cc_start: 0.6030 (OUTLIER) cc_final: 0.5736 (tt0) REVERT: E 402 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7120 (pt0) REVERT: F 11 LYS cc_start: 0.7334 (mmmt) cc_final: 0.7036 (mppt) REVERT: F 224 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7245 (pt0) REVERT: F 227 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7361 (mm) REVERT: F 281 TRP cc_start: 0.5817 (t60) cc_final: 0.5549 (t60) REVERT: F 292 GLU cc_start: 0.6020 (OUTLIER) cc_final: 0.5775 (tt0) outliers start: 173 outliers final: 90 residues processed: 434 average time/residue: 1.4275 time to fit residues: 703.3726 Evaluate side-chains 427 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 316 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 254 ASN Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 254 ASN Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 362 GLU Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 254 ASN Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 435 GLU Chi-restraints excluded: chain F residue 501 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 211 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 chunk 242 optimal weight: 3.9990 chunk 196 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 255 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 330 GLN B 254 ASN B 330 GLN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN C 330 GLN C 374 ASN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 ASN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN F 330 GLN F 374 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23790 Z= 0.195 Angle : 0.532 6.823 32118 Z= 0.288 Chirality : 0.044 0.137 3492 Planarity : 0.004 0.039 4182 Dihedral : 5.968 50.648 3298 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.09 % Allowed : 19.39 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.95 (0.15), residues: 2964 helix: 2.07 (0.13), residues: 1584 sheet: -0.25 (0.27), residues: 384 loop : -1.43 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 385 HIS 0.008 0.001 HIS A 264 PHE 0.028 0.002 PHE C 360 TYR 0.012 0.001 TYR A 407 ARG 0.003 0.000 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 314 time to evaluate : 2.550 Fit side-chains REVERT: A 25 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6138 (tt0) REVERT: A 254 ASN cc_start: 0.7442 (OUTLIER) cc_final: 0.7076 (m-40) REVERT: A 292 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5722 (tt0) REVERT: A 342 LYS cc_start: 0.5511 (mmpt) cc_final: 0.5122 (mmtt) REVERT: A 357 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.7001 (m-30) REVERT: A 419 ARG cc_start: 0.6703 (ttp-110) cc_final: 0.6391 (ttm110) REVERT: B 269 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6956 (ptpp) REVERT: C 11 LYS cc_start: 0.7319 (mmmt) cc_final: 0.7014 (mppt) REVERT: C 25 GLU cc_start: 0.6586 (OUTLIER) cc_final: 0.6202 (tt0) REVERT: C 224 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7194 (pt0) REVERT: C 342 LYS cc_start: 0.5465 (mmpt) cc_final: 0.4710 (mttp) REVERT: D 254 ASN cc_start: 0.7443 (OUTLIER) cc_final: 0.7075 (m-40) REVERT: D 292 GLU cc_start: 0.5997 (OUTLIER) cc_final: 0.5707 (tt0) REVERT: D 340 LYS cc_start: 0.5721 (OUTLIER) cc_final: 0.4648 (mmtp) REVERT: D 342 LYS cc_start: 0.5453 (mmpt) cc_final: 0.5018 (mmtt) REVERT: D 357 ASP cc_start: 0.7244 (OUTLIER) cc_final: 0.6977 (m-30) REVERT: F 25 GLU cc_start: 0.6586 (OUTLIER) cc_final: 0.6203 (tt0) REVERT: F 224 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7187 (pt0) outliers start: 127 outliers final: 72 residues processed: 386 average time/residue: 1.4277 time to fit residues: 629.1365 Evaluate side-chains 392 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 307 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 254 ASN Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 254 ASN Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 254 ASN Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 435 GLU Chi-restraints excluded: chain F residue 501 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 5.9990 chunk 255 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 284 optimal weight: 2.9990 chunk 236 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 374 ASN B 254 ASN C 254 ASN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN D 374 ASN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 ASN F 254 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23790 Z= 0.283 Angle : 0.600 7.888 32118 Z= 0.323 Chirality : 0.046 0.146 3492 Planarity : 0.005 0.051 4182 Dihedral : 6.250 50.900 3294 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.65 % Allowed : 18.91 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.69 (0.15), residues: 2964 helix: 1.86 (0.13), residues: 1584 sheet: -0.39 (0.27), residues: 396 loop : -1.55 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 385 HIS 0.007 0.002 HIS A 264 PHE 0.026 0.002 PHE C 360 TYR 0.012 0.002 TYR D 407 ARG 0.004 0.001 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 313 time to evaluate : 2.502 Fit side-chains REVERT: A 25 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6229 (tt0) REVERT: A 110 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8676 (tm) REVERT: A 292 GLU cc_start: 0.6119 (OUTLIER) cc_final: 0.5824 (tt0) REVERT: A 340 LYS cc_start: 0.5905 (OUTLIER) cc_final: 0.4997 (mmtp) REVERT: A 342 LYS cc_start: 0.5548 (mmpt) cc_final: 0.5059 (mmtt) REVERT: A 357 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6998 (m-30) REVERT: A 418 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6550 (mt-10) REVERT: A 419 ARG cc_start: 0.6726 (ttp-110) cc_final: 0.6386 (ttm110) REVERT: B 44 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6523 (ttt-90) REVERT: B 269 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6908 (ptpp) REVERT: B 402 GLU cc_start: 0.7330 (pt0) cc_final: 0.7074 (pt0) REVERT: C 11 LYS cc_start: 0.7328 (mmmt) cc_final: 0.7030 (mppt) REVERT: C 25 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6265 (tt0) REVERT: C 224 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7238 (pt0) REVERT: C 292 GLU cc_start: 0.5996 (OUTLIER) cc_final: 0.5767 (tt0) REVERT: D 25 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6200 (tt0) REVERT: D 110 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8676 (tm) REVERT: D 292 GLU cc_start: 0.6123 (OUTLIER) cc_final: 0.5827 (tt0) REVERT: D 340 LYS cc_start: 0.5827 (OUTLIER) cc_final: 0.4932 (mmtp) REVERT: D 342 LYS cc_start: 0.5477 (mmpt) cc_final: 0.5073 (mmtt) REVERT: D 357 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.7018 (m-30) REVERT: E 44 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6478 (ttt-90) REVERT: E 292 GLU cc_start: 0.5983 (OUTLIER) cc_final: 0.5683 (tt0) REVERT: E 402 GLU cc_start: 0.7329 (pt0) cc_final: 0.7069 (pt0) REVERT: F 25 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6264 (tt0) REVERT: F 224 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7228 (pt0) REVERT: F 292 GLU cc_start: 0.6003 (OUTLIER) cc_final: 0.5766 (tt0) outliers start: 141 outliers final: 81 residues processed: 399 average time/residue: 1.3606 time to fit residues: 619.8335 Evaluate side-chains 410 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 308 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 254 ASN Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 362 GLU Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 254 ASN Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 292 GLU Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 435 GLU Chi-restraints excluded: chain F residue 501 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 162 optimal weight: 0.8980 chunk 207 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 158 optimal weight: 0.0980 chunk 283 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23790 Z= 0.216 Angle : 0.552 7.788 32118 Z= 0.297 Chirality : 0.044 0.138 3492 Planarity : 0.005 0.039 4182 Dihedral : 6.005 52.110 3294 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.41 % Allowed : 19.87 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.88 (0.15), residues: 2964 helix: 2.03 (0.13), residues: 1584 sheet: -0.24 (0.27), residues: 384 loop : -1.52 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 385 HIS 0.008 0.001 HIS A 264 PHE 0.026 0.002 PHE C 360 TYR 0.013 0.001 TYR D 407 ARG 0.003 0.000 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 308 time to evaluate : 2.734 Fit side-chains REVERT: A 25 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6195 (tt0) REVERT: A 110 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8631 (tm) REVERT: A 292 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5756 (tt0) REVERT: A 340 LYS cc_start: 0.5858 (OUTLIER) cc_final: 0.4784 (mmtp) REVERT: A 342 LYS cc_start: 0.5492 (mmpt) cc_final: 0.5053 (mmtt) REVERT: A 357 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.6983 (m-30) REVERT: A 419 ARG cc_start: 0.6773 (ttp-110) cc_final: 0.6434 (ttm110) REVERT: B 269 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6879 (ptpp) REVERT: B 402 GLU cc_start: 0.7310 (pt0) cc_final: 0.7067 (pt0) REVERT: C 25 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6211 (tt0) REVERT: C 224 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7187 (pt0) REVERT: C 328 GLU cc_start: 0.5292 (OUTLIER) cc_final: 0.4501 (pp20) REVERT: C 342 LYS cc_start: 0.5555 (mmpt) cc_final: 0.4695 (mttp) REVERT: D 110 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8627 (tm) REVERT: D 292 GLU cc_start: 0.6030 (OUTLIER) cc_final: 0.5736 (tt0) REVERT: D 340 LYS cc_start: 0.5757 (OUTLIER) cc_final: 0.4692 (mmtp) REVERT: D 342 LYS cc_start: 0.5419 (mmpt) cc_final: 0.5002 (mmtt) REVERT: D 357 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6978 (m-30) REVERT: E 292 GLU cc_start: 0.5950 (OUTLIER) cc_final: 0.5654 (tt0) REVERT: E 402 GLU cc_start: 0.7297 (pt0) cc_final: 0.7055 (pt0) REVERT: F 224 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7179 (pt0) REVERT: F 328 GLU cc_start: 0.5315 (OUTLIER) cc_final: 0.4504 (pp20) REVERT: F 342 LYS cc_start: 0.5513 (mmpt) cc_final: 0.4647 (mttp) outliers start: 110 outliers final: 74 residues processed: 375 average time/residue: 1.4412 time to fit residues: 615.7691 Evaluate side-chains 396 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 306 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 254 ASN Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 254 ASN Chi-restraints excluded: chain F residue 269 LYS Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 435 GLU Chi-restraints excluded: chain F residue 501 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 169 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 222 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 330 GLN A 374 ASN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN C 374 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN D 374 ASN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN F 374 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23790 Z= 0.186 Angle : 0.527 8.840 32118 Z= 0.283 Chirality : 0.043 0.133 3492 Planarity : 0.004 0.037 4182 Dihedral : 5.772 52.843 3292 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.37 % Allowed : 19.91 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.01 (0.15), residues: 2964 helix: 2.16 (0.13), residues: 1584 sheet: -0.61 (0.26), residues: 414 loop : -1.32 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 385 HIS 0.008 0.001 HIS A 264 PHE 0.025 0.002 PHE C 360 TYR 0.014 0.001 TYR A 407 ARG 0.002 0.000 ARG F 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 306 time to evaluate : 2.597 Fit side-chains REVERT: A 110 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8613 (tm) REVERT: A 292 GLU cc_start: 0.5955 (OUTLIER) cc_final: 0.5668 (tt0) REVERT: A 340 LYS cc_start: 0.5769 (OUTLIER) cc_final: 0.4693 (mmtp) REVERT: A 342 LYS cc_start: 0.5322 (mmpt) cc_final: 0.4772 (mttp) REVERT: A 357 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.7011 (m-30) REVERT: A 419 ARG cc_start: 0.6733 (ttp-110) cc_final: 0.6451 (ttm110) REVERT: B 269 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6900 (ptpp) REVERT: B 402 GLU cc_start: 0.7329 (pt0) cc_final: 0.7063 (pt0) REVERT: C 11 LYS cc_start: 0.7279 (mmmt) cc_final: 0.7029 (mppt) REVERT: C 25 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6207 (tt0) REVERT: C 224 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7203 (pt0) REVERT: C 292 GLU cc_start: 0.5938 (OUTLIER) cc_final: 0.5666 (tt0) REVERT: C 328 GLU cc_start: 0.5251 (OUTLIER) cc_final: 0.4517 (pp20) REVERT: C 342 LYS cc_start: 0.5456 (mmpt) cc_final: 0.4658 (mttp) REVERT: D 110 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8611 (tm) REVERT: D 292 GLU cc_start: 0.5946 (OUTLIER) cc_final: 0.5656 (tt0) REVERT: D 340 LYS cc_start: 0.5729 (OUTLIER) cc_final: 0.4655 (mmtp) REVERT: D 342 LYS cc_start: 0.5384 (mmpt) cc_final: 0.4974 (mmtt) REVERT: D 357 ASP cc_start: 0.7238 (OUTLIER) cc_final: 0.7006 (m-30) REVERT: E 292 GLU cc_start: 0.5970 (OUTLIER) cc_final: 0.5637 (tt0) REVERT: E 402 GLU cc_start: 0.7325 (pt0) cc_final: 0.7058 (pt0) REVERT: F 11 LYS cc_start: 0.7306 (mmmt) cc_final: 0.7038 (mppt) REVERT: F 224 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7191 (pt0) REVERT: F 328 GLU cc_start: 0.5285 (OUTLIER) cc_final: 0.4472 (pp20) outliers start: 109 outliers final: 72 residues processed: 366 average time/residue: 1.4852 time to fit residues: 614.4696 Evaluate side-chains 390 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 302 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 254 ASN Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 435 GLU Chi-restraints excluded: chain F residue 501 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 5.9990 chunk 271 optimal weight: 0.8980 chunk 247 optimal weight: 0.0870 chunk 264 optimal weight: 9.9990 chunk 158 optimal weight: 0.4980 chunk 115 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 238 optimal weight: 10.0000 chunk 249 optimal weight: 2.9990 chunk 263 optimal weight: 0.6980 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN B 254 ASN B 374 ASN B 463 GLN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN E 254 ASN E 374 ASN E 463 GLN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23790 Z= 0.147 Angle : 0.491 9.745 32118 Z= 0.263 Chirality : 0.042 0.133 3492 Planarity : 0.004 0.034 4182 Dihedral : 5.363 53.388 3288 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.65 % Allowed : 20.79 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.18 (0.16), residues: 2964 helix: 2.34 (0.13), residues: 1584 sheet: -0.63 (0.25), residues: 414 loop : -1.26 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 72 HIS 0.009 0.001 HIS A 264 PHE 0.027 0.001 PHE C 360 TYR 0.014 0.001 TYR A 407 ARG 0.002 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 300 time to evaluate : 2.633 Fit side-chains REVERT: A 110 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8588 (tm) REVERT: A 342 LYS cc_start: 0.5131 (mmpt) cc_final: 0.4642 (mttp) REVERT: A 357 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6997 (m-30) REVERT: A 419 ARG cc_start: 0.6635 (ttp-110) cc_final: 0.6395 (ttm110) REVERT: B 346 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6667 (mt-10) REVERT: C 11 LYS cc_start: 0.7269 (mmmt) cc_final: 0.6993 (mppt) REVERT: C 25 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6147 (tt0) REVERT: C 328 GLU cc_start: 0.5199 (OUTLIER) cc_final: 0.4444 (pp20) REVERT: D 110 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8586 (tm) REVERT: D 342 LYS cc_start: 0.5253 (mmpt) cc_final: 0.4811 (mmtt) REVERT: D 357 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.6989 (m-30) REVERT: E 346 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6657 (mt-10) REVERT: E 402 GLU cc_start: 0.7305 (pt0) cc_final: 0.7050 (pt0) REVERT: F 11 LYS cc_start: 0.7274 (mmmt) cc_final: 0.7008 (mppt) REVERT: F 328 GLU cc_start: 0.5198 (OUTLIER) cc_final: 0.4439 (pp20) outliers start: 91 outliers final: 56 residues processed: 348 average time/residue: 1.5653 time to fit residues: 623.4887 Evaluate side-chains 359 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 296 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 254 ASN Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 435 GLU Chi-restraints excluded: chain F residue 501 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 10.0000 chunk 279 optimal weight: 0.5980 chunk 170 optimal weight: 7.9990 chunk 132 optimal weight: 0.3980 chunk 194 optimal weight: 1.9990 chunk 292 optimal weight: 0.3980 chunk 269 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 180 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 374 ASN B 254 ASN B 463 GLN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN C 374 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN D 374 ASN E 254 ASN E 463 GLN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23790 Z= 0.139 Angle : 0.486 9.115 32118 Z= 0.258 Chirality : 0.042 0.135 3492 Planarity : 0.004 0.033 4182 Dihedral : 4.950 52.682 3280 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.92 % Allowed : 21.59 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.39 (0.16), residues: 2964 helix: 2.56 (0.13), residues: 1542 sheet: -0.69 (0.25), residues: 414 loop : -1.02 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 72 HIS 0.009 0.001 HIS A 264 PHE 0.027 0.001 PHE C 360 TYR 0.015 0.001 TYR D 407 ARG 0.002 0.000 ARG D 217 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 310 time to evaluate : 2.684 Fit side-chains REVERT: A 110 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8580 (tm) REVERT: A 342 LYS cc_start: 0.5072 (mmpt) cc_final: 0.4607 (mttp) REVERT: A 357 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6983 (m-30) REVERT: A 415 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7172 (mt-10) REVERT: B 340 LYS cc_start: 0.5586 (mmtp) cc_final: 0.5182 (ptmt) REVERT: C 11 LYS cc_start: 0.7269 (mmmt) cc_final: 0.6991 (mppt) REVERT: C 25 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.6144 (tt0) REVERT: C 328 GLU cc_start: 0.5102 (OUTLIER) cc_final: 0.4355 (pp20) REVERT: D 110 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8578 (tm) REVERT: D 342 LYS cc_start: 0.5160 (mmpt) cc_final: 0.4724 (mmtt) REVERT: D 357 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6977 (m-30) REVERT: E 340 LYS cc_start: 0.5460 (mmtp) cc_final: 0.4955 (ptmt) REVERT: E 342 LYS cc_start: 0.5126 (mmpt) cc_final: 0.4533 (mmpt) REVERT: E 419 ARG cc_start: 0.6677 (ttp-110) cc_final: 0.6458 (ttm110) REVERT: F 11 LYS cc_start: 0.7276 (mmmt) cc_final: 0.7006 (mppt) REVERT: F 25 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.6142 (tt0) REVERT: F 340 LYS cc_start: 0.5538 (mmtp) cc_final: 0.5020 (ptmt) REVERT: F 342 LYS cc_start: 0.5402 (mmpt) cc_final: 0.4792 (mttm) outliers start: 73 outliers final: 41 residues processed: 349 average time/residue: 1.4743 time to fit residues: 581.8669 Evaluate side-chains 340 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 292 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 501 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 215 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 233 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 239 optimal weight: 9.9990 chunk 29 optimal weight: 0.0980 chunk 43 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN B 254 ASN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN E 254 ASN E 463 GLN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.176310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.136502 restraints weight = 24415.185| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.32 r_work: 0.3470 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23790 Z= 0.161 Angle : 0.508 9.074 32118 Z= 0.271 Chirality : 0.042 0.137 3492 Planarity : 0.004 0.033 4182 Dihedral : 4.641 51.490 3272 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.52 % Allowed : 22.08 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.18 (0.15), residues: 2964 helix: 2.32 (0.13), residues: 1584 sheet: -0.65 (0.25), residues: 414 loop : -1.21 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 385 HIS 0.010 0.001 HIS A 264 PHE 0.029 0.001 PHE C 360 TYR 0.015 0.001 TYR D 407 ARG 0.002 0.000 ARG A 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10535.74 seconds wall clock time: 186 minutes 31.96 seconds (11191.96 seconds total)