Starting phenix.real_space_refine on Sat Jul 20 19:45:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvu_42629/07_2024/8uvu_42629.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvu_42629/07_2024/8uvu_42629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvu_42629/07_2024/8uvu_42629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvu_42629/07_2024/8uvu_42629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvu_42629/07_2024/8uvu_42629.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uvu_42629/07_2024/8uvu_42629.cif" } resolution = 3.0 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= 0.003 sd= 0.102 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 120 5.16 5 C 7784 2.51 5 N 2000 2.21 5 O 2072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 423": "OD1" <-> "OD2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 423": "OD1" <-> "OD2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "C TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 423": "OD1" <-> "OD2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 423": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11976 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2970 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2970 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2970 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2970 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 24 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 12 Unusual residues: {'BDF': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 24 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 12 Unusual residues: {'BDF': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 24 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 12 Unusual residues: {'BDF': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 12 Unusual residues: {'BDF': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" C1 ABDF A 501 " occ=0.75 ... (10 atoms not shown) pdb=" O6 ABDF A 501 " occ=0.75 residue: pdb=" C1 BFRU A 502 " occ=0.25 ... (10 atoms not shown) pdb=" O6 BFRU A 502 " occ=0.25 residue: pdb=" C1 ABDF B 501 " occ=0.75 ... (10 atoms not shown) pdb=" O6 ABDF B 501 " occ=0.75 residue: pdb=" C1 BFRU B 502 " occ=0.25 ... (10 atoms not shown) pdb=" O6 BFRU B 502 " occ=0.25 residue: pdb=" C1 ABDF C 501 " occ=0.75 ... (10 atoms not shown) pdb=" O6 ABDF C 501 " occ=0.75 residue: pdb=" C1 BFRU C 502 " occ=0.25 ... (10 atoms not shown) pdb=" O6 BFRU C 502 " occ=0.25 residue: pdb=" C1 ABDF D 501 " occ=0.75 ... (10 atoms not shown) pdb=" O6 ABDF D 501 " occ=0.75 residue: pdb=" C1 BFRU D 502 " occ=0.25 ... (10 atoms not shown) pdb=" O6 BFRU D 502 " occ=0.25 Time building chain proxies: 4.55, per 1000 atoms: 0.38 Number of scatterers: 11976 At special positions: 0 Unit cell: (110.004, 110.004, 93.984, 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 120 16.00 O 2072 8.00 N 2000 7.00 C 7784 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: 5.26 Conformation dependent library (CDL) restraints added in 2.1 seconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2856 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 85.5% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 removed outlier: 3.817A pdb=" N PHE A 24 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU A 26 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 79 removed outlier: 3.531A pdb=" N TYR A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 112 removed outlier: 4.100A pdb=" N VAL A 94 " --> pdb=" O ARG A 90 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 95 " --> pdb=" O MET A 91 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 134 removed outlier: 3.916A pdb=" N GLU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 176 removed outlier: 3.773A pdb=" N SER A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 147 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA A 149 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 175 " --> pdb=" O MET A 171 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR A 176 " --> pdb=" O GLN A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 186 Processing helix chain 'A' and resid 186 through 225 removed outlier: 4.051A pdb=" N TYR A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 341 removed outlier: 3.645A pdb=" N GLY A 292 " --> pdb=" O CYS A 288 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Proline residue: A 315 - end of helix Proline residue: A 331 - end of helix Processing helix chain 'A' and resid 344 through 390 Proline residue: A 368 - end of helix Processing helix chain 'A' and resid 394 through 410 removed outlier: 4.121A pdb=" N SER A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 423 through 446 removed outlier: 3.708A pdb=" N MET A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 removed outlier: 3.816A pdb=" N PHE B 24 " --> pdb=" O GLY B 20 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU B 26 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 79 removed outlier: 3.532A pdb=" N TYR B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 112 removed outlier: 4.100A pdb=" N VAL B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 95 " --> pdb=" O MET B 91 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 134 removed outlier: 3.916A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 134 " --> pdb=" O ALA B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 176 removed outlier: 3.773A pdb=" N SER B 140 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR B 176 " --> pdb=" O GLN B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 186 Processing helix chain 'B' and resid 186 through 225 removed outlier: 4.052A pdb=" N TYR B 190 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 341 removed outlier: 3.645A pdb=" N GLY B 292 " --> pdb=" O CYS B 288 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Proline residue: B 315 - end of helix Proline residue: B 331 - end of helix Processing helix chain 'B' and resid 344 through 390 Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 394 through 410 removed outlier: 4.122A pdb=" N SER B 398 " --> pdb=" O GLY B 394 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 399 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 423 through 446 removed outlier: 3.708A pdb=" N MET B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 32 removed outlier: 3.817A pdb=" N PHE C 24 " --> pdb=" O GLY C 20 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU C 26 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS C 27 " --> pdb=" O ALA C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 79 removed outlier: 3.532A pdb=" N TYR C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 112 removed outlier: 4.100A pdb=" N VAL C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 95 " --> pdb=" O MET C 91 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 134 removed outlier: 3.917A pdb=" N GLU C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA C 130 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU C 134 " --> pdb=" O ALA C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 176 removed outlier: 3.773A pdb=" N SER C 140 " --> pdb=" O GLY C 136 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 147 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA C 149 " --> pdb=" O ARG C 145 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS C 175 " --> pdb=" O MET C 171 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR C 176 " --> pdb=" O GLN C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 186 Processing helix chain 'C' and resid 186 through 225 removed outlier: 4.051A pdb=" N TYR C 190 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 341 removed outlier: 3.646A pdb=" N GLY C 292 " --> pdb=" O CYS C 288 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU C 314 " --> pdb=" O ASP C 310 " (cutoff:3.500A) Proline residue: C 315 - end of helix Proline residue: C 331 - end of helix Processing helix chain 'C' and resid 344 through 390 Proline residue: C 368 - end of helix Processing helix chain 'C' and resid 394 through 410 removed outlier: 4.122A pdb=" N SER C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG C 399 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 423 through 446 removed outlier: 3.708A pdb=" N MET C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 32 removed outlier: 3.817A pdb=" N PHE D 24 " --> pdb=" O GLY D 20 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU D 26 " --> pdb=" O HIS D 22 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 79 removed outlier: 3.533A pdb=" N TYR D 57 " --> pdb=" O GLY D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 112 removed outlier: 4.100A pdb=" N VAL D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL D 95 " --> pdb=" O MET D 91 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 134 removed outlier: 3.916A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU D 134 " --> pdb=" O ALA D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 176 removed outlier: 3.774A pdb=" N SER D 140 " --> pdb=" O GLY D 136 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 147 " --> pdb=" O THR D 143 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU D 150 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 175 " --> pdb=" O MET D 171 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR D 176 " --> pdb=" O GLN D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 186 Processing helix chain 'D' and resid 186 through 225 removed outlier: 4.052A pdb=" N TYR D 190 " --> pdb=" O TYR D 186 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 341 removed outlier: 3.646A pdb=" N GLY D 292 " --> pdb=" O CYS D 288 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU D 314 " --> pdb=" O ASP D 310 " (cutoff:3.500A) Proline residue: D 315 - end of helix Proline residue: D 331 - end of helix Processing helix chain 'D' and resid 344 through 390 Proline residue: D 368 - end of helix Processing helix chain 'D' and resid 394 through 410 removed outlier: 4.121A pdb=" N SER D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG D 399 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 423 through 446 removed outlier: 3.708A pdb=" N MET D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 18 removed outlier: 4.267A pdb=" N CYS A 16 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A 49 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 16 through 18 removed outlier: 4.268A pdb=" N CYS B 16 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR B 49 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 16 through 18 removed outlier: 4.268A pdb=" N CYS C 16 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR C 49 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 16 through 18 removed outlier: 4.269A pdb=" N CYS D 16 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR D 49 " --> pdb=" O ARG D 38 " (cutoff:3.500A) 984 hydrogen bonds defined for protein. 2916 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: 3.56 Time building geometry restraints manager: 5.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3716 1.34 - 1.46: 2834 1.46 - 1.58: 5478 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 12208 Sorted by residual: bond pdb=" C2 BFRU B 502 " pdb=" O2 BFRU B 502 " ideal model delta sigma weight residual 1.388 1.426 -0.038 2.00e-02 2.50e+03 3.66e+00 bond pdb=" C2 BFRU A 502 " pdb=" O2 BFRU A 502 " ideal model delta sigma weight residual 1.388 1.426 -0.038 2.00e-02 2.50e+03 3.57e+00 bond pdb=" C2 BFRU C 502 " pdb=" O2 BFRU C 502 " ideal model delta sigma weight residual 1.388 1.426 -0.038 2.00e-02 2.50e+03 3.56e+00 bond pdb=" C2 BFRU D 502 " pdb=" O2 BFRU D 502 " ideal model delta sigma weight residual 1.388 1.425 -0.037 2.00e-02 2.50e+03 3.49e+00 bond pdb=" C2 ABDF A 501 " pdb=" O2 ABDF A 501 " ideal model delta sigma weight residual 1.390 1.425 -0.035 2.00e-02 2.50e+03 3.07e+00 ... (remaining 12203 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.35: 292 106.35 - 113.29: 7041 113.29 - 120.23: 4263 120.23 - 127.17: 4872 127.17 - 134.10: 116 Bond angle restraints: 16584 Sorted by residual: angle pdb=" N ALA B 23 " pdb=" CA ALA B 23 " pdb=" C ALA B 23 " ideal model delta sigma weight residual 114.62 108.80 5.82 1.14e+00 7.69e-01 2.61e+01 angle pdb=" N ALA A 23 " pdb=" CA ALA A 23 " pdb=" C ALA A 23 " ideal model delta sigma weight residual 114.62 108.83 5.79 1.14e+00 7.69e-01 2.58e+01 angle pdb=" N ALA D 23 " pdb=" CA ALA D 23 " pdb=" C ALA D 23 " ideal model delta sigma weight residual 114.62 108.83 5.79 1.14e+00 7.69e-01 2.58e+01 angle pdb=" N ALA C 23 " pdb=" CA ALA C 23 " pdb=" C ALA C 23 " ideal model delta sigma weight residual 114.62 108.86 5.76 1.14e+00 7.69e-01 2.55e+01 angle pdb=" CA ALA A 23 " pdb=" C ALA A 23 " pdb=" N PHE A 24 " ideal model delta sigma weight residual 119.71 116.12 3.59 1.17e+00 7.31e-01 9.41e+00 ... (remaining 16579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6640 17.96 - 35.91: 599 35.91 - 53.87: 145 53.87 - 71.82: 32 71.82 - 89.78: 8 Dihedral angle restraints: 7424 sinusoidal: 3000 harmonic: 4424 Sorted by residual: dihedral pdb=" CA LYS D 52 " pdb=" C LYS D 52 " pdb=" N GLY D 53 " pdb=" CA GLY D 53 " ideal model delta harmonic sigma weight residual -180.00 -163.65 -16.35 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA LYS A 52 " pdb=" C LYS A 52 " pdb=" N GLY A 53 " pdb=" CA GLY A 53 " ideal model delta harmonic sigma weight residual -180.00 -163.67 -16.33 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA LYS C 52 " pdb=" C LYS C 52 " pdb=" N GLY C 53 " pdb=" CA GLY C 53 " ideal model delta harmonic sigma weight residual -180.00 -163.68 -16.32 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 7421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1846 0.062 - 0.124: 186 0.124 - 0.186: 8 0.186 - 0.248: 8 0.248 - 0.309: 4 Chirality restraints: 2052 Sorted by residual: chirality pdb=" C3 BFRU A 502 " pdb=" C2 BFRU A 502 " pdb=" C4 BFRU A 502 " pdb=" O3 BFRU A 502 " both_signs ideal model delta sigma weight residual False 2.47 2.78 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C3 BFRU C 502 " pdb=" C2 BFRU C 502 " pdb=" C4 BFRU C 502 " pdb=" O3 BFRU C 502 " both_signs ideal model delta sigma weight residual False 2.47 2.78 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C3 BFRU B 502 " pdb=" C2 BFRU B 502 " pdb=" C4 BFRU B 502 " pdb=" O3 BFRU B 502 " both_signs ideal model delta sigma weight residual False 2.47 2.78 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 2049 not shown) Planarity restraints: 1992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 285 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO D 286 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 286 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 286 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 285 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A 286 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 286 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 286 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 285 " -0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO C 286 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 286 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 286 " -0.019 5.00e-02 4.00e+02 ... (remaining 1989 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2385 2.78 - 3.31: 12351 3.31 - 3.84: 20664 3.84 - 4.37: 23759 4.37 - 4.90: 42018 Nonbonded interactions: 101177 Sorted by model distance: nonbonded pdb=" OD1 ASN A 218 " pdb=" OG1 THR A 379 " model vdw 2.246 2.440 nonbonded pdb=" OD1 ASN B 218 " pdb=" OG1 THR B 379 " model vdw 2.246 2.440 nonbonded pdb=" OD1 ASN D 218 " pdb=" OG1 THR D 379 " model vdw 2.246 2.440 nonbonded pdb=" OD1 ASN C 218 " pdb=" OG1 THR C 379 " model vdw 2.246 2.440 nonbonded pdb=" N GLN B 179 " pdb=" OE1 GLN B 179 " model vdw 2.256 2.520 ... (remaining 101172 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' and resid 14 through 446) selection = (chain 'B' and resid 14 through 446) selection = (chain 'C' and resid 14 through 446) selection = (chain 'D' and resid 14 through 446) } 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=0.25 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: 8.820 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 34.420 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 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 0.038 12208 Z= 0.209 Angle : 0.601 9.182 16584 Z= 0.304 Chirality : 0.041 0.309 2052 Planarity : 0.004 0.035 1992 Dihedral : 14.700 89.777 4568 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.22), residues: 1500 helix: 2.06 (0.14), residues: 1224 sheet: -4.55 (0.58), residues: 44 loop : -2.92 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 193 HIS 0.002 0.000 HIS D 307 PHE 0.014 0.001 PHE C 189 TYR 0.019 0.001 TYR D 124 ARG 0.005 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.255 Fit side-chains REVERT: A 389 LEU cc_start: 0.8293 (mt) cc_final: 0.8018 (mt) REVERT: B 121 MET cc_start: 0.8756 (tmm) cc_final: 0.8540 (tmt) REVERT: B 389 LEU cc_start: 0.8310 (mt) cc_final: 0.8022 (mt) REVERT: C 389 LEU cc_start: 0.8322 (mt) cc_final: 0.8045 (mt) REVERT: D 389 LEU cc_start: 0.8328 (mt) cc_final: 0.8062 (mt) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 1.3215 time to fit residues: 315.8448 Evaluate side-chains 178 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 410 GLN B 222 ASN B 410 GLN C 222 ASN C 410 GLN D 222 ASN D 410 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12208 Z= 0.268 Angle : 0.563 6.612 16584 Z= 0.289 Chirality : 0.038 0.130 2052 Planarity : 0.004 0.034 1992 Dihedral : 4.000 15.488 1856 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.74 % Allowed : 8.71 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.22), residues: 1500 helix: 2.42 (0.14), residues: 1224 sheet: -4.43 (0.55), residues: 44 loop : -3.19 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 193 HIS 0.002 0.001 HIS D 358 PHE 0.014 0.001 PHE B 203 TYR 0.018 0.001 TYR D 124 ARG 0.003 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 181 time to evaluate : 1.346 Fit side-chains REVERT: A 389 LEU cc_start: 0.8592 (mt) cc_final: 0.8338 (mt) REVERT: B 121 MET cc_start: 0.8828 (tmm) cc_final: 0.8605 (tmt) REVERT: B 129 VAL cc_start: 0.7899 (t) cc_final: 0.7449 (m) REVERT: B 389 LEU cc_start: 0.8592 (mt) cc_final: 0.8338 (mt) REVERT: C 129 VAL cc_start: 0.7885 (t) cc_final: 0.7451 (m) REVERT: C 389 LEU cc_start: 0.8610 (mt) cc_final: 0.8363 (mt) REVERT: D 129 VAL cc_start: 0.7887 (t) cc_final: 0.7446 (m) REVERT: D 389 LEU cc_start: 0.8610 (mt) cc_final: 0.8362 (mt) outliers start: 23 outliers final: 12 residues processed: 199 average time/residue: 1.3310 time to fit residues: 287.0169 Evaluate side-chains 192 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 180 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 222 ASN C 222 ASN D 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12208 Z= 0.294 Angle : 0.579 7.187 16584 Z= 0.294 Chirality : 0.038 0.141 2052 Planarity : 0.004 0.036 1992 Dihedral : 4.068 16.298 1856 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.12 % Allowed : 11.67 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.22), residues: 1500 helix: 2.38 (0.14), residues: 1224 sheet: -4.36 (0.55), residues: 44 loop : -3.17 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 193 HIS 0.003 0.001 HIS B 326 PHE 0.015 0.001 PHE B 205 TYR 0.020 0.002 TYR A 124 ARG 0.003 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 1.645 Fit side-chains REVERT: A 129 VAL cc_start: 0.7914 (t) cc_final: 0.7389 (m) REVERT: A 389 LEU cc_start: 0.8654 (mt) cc_final: 0.8409 (mt) REVERT: B 121 MET cc_start: 0.8826 (tmm) cc_final: 0.8582 (tmt) REVERT: B 129 VAL cc_start: 0.7928 (t) cc_final: 0.7397 (m) REVERT: B 389 LEU cc_start: 0.8653 (mt) cc_final: 0.8409 (mt) REVERT: C 129 VAL cc_start: 0.7917 (t) cc_final: 0.7396 (m) REVERT: C 389 LEU cc_start: 0.8682 (mt) cc_final: 0.8441 (mt) REVERT: D 129 VAL cc_start: 0.7920 (t) cc_final: 0.7390 (m) REVERT: D 389 LEU cc_start: 0.8679 (mt) cc_final: 0.8435 (mt) outliers start: 28 outliers final: 20 residues processed: 197 average time/residue: 1.2964 time to fit residues: 276.9331 Evaluate side-chains 197 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 177 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 69 optimal weight: 0.0020 chunk 14 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 135 optimal weight: 0.6980 chunk 143 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 392 HIS B 222 ASN B 392 HIS C 222 ASN C 392 HIS D 222 ASN D 392 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12208 Z= 0.212 Angle : 0.532 7.569 16584 Z= 0.273 Chirality : 0.036 0.123 2052 Planarity : 0.004 0.037 1992 Dihedral : 3.964 18.382 1856 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.12 % Allowed : 13.26 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.22), residues: 1500 helix: 2.55 (0.14), residues: 1224 sheet: -4.31 (0.55), residues: 44 loop : -3.04 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.003 0.001 HIS B 22 PHE 0.015 0.001 PHE D 205 TYR 0.018 0.001 TYR A 124 ARG 0.002 0.000 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 178 time to evaluate : 1.345 Fit side-chains REVERT: A 129 VAL cc_start: 0.7898 (t) cc_final: 0.7346 (m) REVERT: A 365 VAL cc_start: 0.8837 (t) cc_final: 0.8503 (t) REVERT: A 389 LEU cc_start: 0.8624 (mt) cc_final: 0.8364 (mt) REVERT: B 121 MET cc_start: 0.8803 (tmm) cc_final: 0.8580 (tmt) REVERT: B 129 VAL cc_start: 0.7917 (t) cc_final: 0.7361 (m) REVERT: B 365 VAL cc_start: 0.8836 (t) cc_final: 0.8501 (t) REVERT: B 389 LEU cc_start: 0.8622 (mt) cc_final: 0.8364 (mt) REVERT: C 129 VAL cc_start: 0.7901 (t) cc_final: 0.7355 (m) REVERT: C 365 VAL cc_start: 0.8835 (t) cc_final: 0.8500 (t) REVERT: C 389 LEU cc_start: 0.8629 (mt) cc_final: 0.8359 (mt) REVERT: D 129 VAL cc_start: 0.7902 (t) cc_final: 0.7349 (m) REVERT: D 365 VAL cc_start: 0.8835 (t) cc_final: 0.8501 (t) REVERT: D 389 LEU cc_start: 0.8626 (mt) cc_final: 0.8394 (mt) outliers start: 28 outliers final: 20 residues processed: 202 average time/residue: 1.3276 time to fit residues: 290.0288 Evaluate side-chains 195 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 175 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 222 ASN C 222 ASN D 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12208 Z= 0.256 Angle : 0.561 7.518 16584 Z= 0.286 Chirality : 0.037 0.134 2052 Planarity : 0.004 0.037 1992 Dihedral : 3.979 18.055 1856 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.03 % Allowed : 14.77 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.22), residues: 1500 helix: 2.48 (0.14), residues: 1228 sheet: -4.29 (0.55), residues: 44 loop : -2.97 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 354 HIS 0.003 0.001 HIS D 22 PHE 0.016 0.001 PHE D 205 TYR 0.019 0.002 TYR C 124 ARG 0.003 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 172 time to evaluate : 1.413 Fit side-chains REVERT: A 365 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8517 (t) REVERT: A 389 LEU cc_start: 0.8667 (mt) cc_final: 0.8441 (mt) REVERT: B 129 VAL cc_start: 0.7910 (t) cc_final: 0.7350 (m) REVERT: B 365 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8515 (t) REVERT: B 389 LEU cc_start: 0.8665 (mt) cc_final: 0.8437 (mt) REVERT: C 365 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8517 (t) REVERT: C 389 LEU cc_start: 0.8674 (mt) cc_final: 0.8449 (mt) REVERT: D 365 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8518 (t) REVERT: D 389 LEU cc_start: 0.8675 (mt) cc_final: 0.8428 (mt) outliers start: 40 outliers final: 20 residues processed: 204 average time/residue: 1.3880 time to fit residues: 305.0221 Evaluate side-chains 195 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 365 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 410 GLN B 222 ASN B 410 GLN C 222 ASN C 410 GLN D 222 ASN D 410 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12208 Z= 0.267 Angle : 0.576 8.662 16584 Z= 0.290 Chirality : 0.038 0.135 2052 Planarity : 0.004 0.038 1992 Dihedral : 4.045 19.849 1856 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.47 % Allowed : 14.24 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.22), residues: 1500 helix: 2.40 (0.14), residues: 1232 sheet: -4.30 (0.55), residues: 44 loop : -3.10 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 354 HIS 0.005 0.001 HIS C 22 PHE 0.014 0.001 PHE B 205 TYR 0.018 0.001 TYR A 124 ARG 0.003 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 174 time to evaluate : 1.398 Fit side-chains REVERT: A 151 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7073 (tp) REVERT: A 365 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8558 (t) REVERT: A 389 LEU cc_start: 0.8613 (mt) cc_final: 0.8378 (mt) REVERT: B 151 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6935 (tp) REVERT: B 365 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8557 (t) REVERT: B 389 LEU cc_start: 0.8646 (mt) cc_final: 0.8423 (mt) REVERT: C 151 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6937 (tp) REVERT: C 365 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8558 (t) REVERT: C 389 LEU cc_start: 0.8621 (mt) cc_final: 0.8390 (mt) REVERT: D 151 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6937 (tp) REVERT: D 365 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8557 (t) REVERT: D 389 LEU cc_start: 0.8620 (mt) cc_final: 0.8384 (mt) outliers start: 59 outliers final: 24 residues processed: 220 average time/residue: 1.2855 time to fit residues: 306.4140 Evaluate side-chains 201 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 169 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 420 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 81 optimal weight: 0.0050 chunk 104 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 410 GLN B 222 ASN B 410 GLN C 222 ASN D 222 ASN D 410 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12208 Z= 0.213 Angle : 0.554 8.586 16584 Z= 0.280 Chirality : 0.036 0.121 2052 Planarity : 0.004 0.038 1992 Dihedral : 3.967 18.151 1856 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.48 % Allowed : 15.38 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.22), residues: 1500 helix: 2.55 (0.14), residues: 1224 sheet: -4.31 (0.55), residues: 44 loop : -3.05 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 193 HIS 0.003 0.001 HIS D 22 PHE 0.014 0.001 PHE B 205 TYR 0.019 0.001 TYR C 124 ARG 0.004 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 174 time to evaluate : 1.330 Fit side-chains REVERT: A 151 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.7067 (tp) REVERT: A 365 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8529 (t) REVERT: A 389 LEU cc_start: 0.8582 (mt) cc_final: 0.8353 (mt) REVERT: B 151 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6949 (tp) REVERT: B 365 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8530 (t) REVERT: B 389 LEU cc_start: 0.8618 (mt) cc_final: 0.8382 (mt) REVERT: C 129 VAL cc_start: 0.7917 (t) cc_final: 0.7374 (m) REVERT: C 151 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.7063 (tp) REVERT: C 365 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8528 (t) REVERT: C 389 LEU cc_start: 0.8564 (mt) cc_final: 0.8339 (mt) REVERT: D 151 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.7064 (tp) REVERT: D 365 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8528 (t) REVERT: D 389 LEU cc_start: 0.8561 (mt) cc_final: 0.8312 (mt) outliers start: 46 outliers final: 24 residues processed: 212 average time/residue: 1.3229 time to fit residues: 303.1691 Evaluate side-chains 203 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 171 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 420 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 90 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 410 GLN B 222 ASN B 410 GLN C 222 ASN C 410 GLN D 222 ASN D 410 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12208 Z= 0.231 Angle : 0.563 8.794 16584 Z= 0.284 Chirality : 0.037 0.125 2052 Planarity : 0.004 0.038 1992 Dihedral : 3.995 19.079 1856 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.48 % Allowed : 16.21 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.22), residues: 1500 helix: 2.53 (0.14), residues: 1224 sheet: -4.32 (0.55), residues: 44 loop : -3.04 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.003 0.001 HIS B 22 PHE 0.015 0.001 PHE B 205 TYR 0.018 0.001 TYR C 124 ARG 0.005 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 173 time to evaluate : 1.407 Fit side-chains REVERT: A 129 VAL cc_start: 0.7944 (t) cc_final: 0.7394 (m) REVERT: A 151 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6971 (tp) REVERT: A 193 TRP cc_start: 0.9502 (OUTLIER) cc_final: 0.7160 (m100) REVERT: A 365 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8549 (t) REVERT: A 389 LEU cc_start: 0.8588 (mt) cc_final: 0.8341 (mt) REVERT: B 193 TRP cc_start: 0.9501 (OUTLIER) cc_final: 0.7159 (m100) REVERT: B 365 VAL cc_start: 0.8857 (OUTLIER) cc_final: 0.8548 (t) REVERT: B 389 LEU cc_start: 0.8572 (mt) cc_final: 0.8338 (mt) REVERT: C 129 VAL cc_start: 0.7920 (t) cc_final: 0.7374 (m) REVERT: C 193 TRP cc_start: 0.9501 (OUTLIER) cc_final: 0.7160 (m100) REVERT: C 365 VAL cc_start: 0.8856 (OUTLIER) cc_final: 0.8545 (t) REVERT: C 389 LEU cc_start: 0.8569 (mt) cc_final: 0.8325 (mt) REVERT: D 129 VAL cc_start: 0.7919 (t) cc_final: 0.7370 (m) REVERT: D 193 TRP cc_start: 0.9500 (OUTLIER) cc_final: 0.7159 (m100) REVERT: D 365 VAL cc_start: 0.8857 (OUTLIER) cc_final: 0.8545 (t) REVERT: D 389 LEU cc_start: 0.8600 (mt) cc_final: 0.8372 (mt) outliers start: 46 outliers final: 24 residues processed: 209 average time/residue: 1.3390 time to fit residues: 301.5003 Evaluate side-chains 203 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 170 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 420 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 120 optimal weight: 0.6980 chunk 125 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN B 222 ASN B 410 GLN C 410 GLN D 222 ASN D 410 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12208 Z= 0.239 Angle : 0.576 8.543 16584 Z= 0.290 Chirality : 0.038 0.167 2052 Planarity : 0.004 0.038 1992 Dihedral : 4.031 18.553 1856 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.95 % Allowed : 16.97 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.22), residues: 1500 helix: 2.48 (0.14), residues: 1228 sheet: -4.33 (0.55), residues: 44 loop : -3.17 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 193 HIS 0.003 0.001 HIS D 22 PHE 0.015 0.001 PHE A 205 TYR 0.018 0.001 TYR C 124 ARG 0.005 0.000 ARG D 306 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 174 time to evaluate : 1.482 Fit side-chains REVERT: A 151 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6988 (tp) REVERT: A 193 TRP cc_start: 0.9503 (OUTLIER) cc_final: 0.7177 (m100) REVERT: A 365 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8556 (t) REVERT: A 389 LEU cc_start: 0.8596 (mt) cc_final: 0.8375 (mt) REVERT: B 193 TRP cc_start: 0.9500 (OUTLIER) cc_final: 0.7177 (m100) REVERT: B 365 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8557 (t) REVERT: B 389 LEU cc_start: 0.8623 (mt) cc_final: 0.8385 (mt) REVERT: C 193 TRP cc_start: 0.9501 (OUTLIER) cc_final: 0.7178 (m100) REVERT: C 365 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8552 (t) REVERT: C 389 LEU cc_start: 0.8594 (mt) cc_final: 0.8374 (mt) REVERT: D 193 TRP cc_start: 0.9500 (OUTLIER) cc_final: 0.7177 (m100) REVERT: D 365 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8554 (t) REVERT: D 389 LEU cc_start: 0.8609 (mt) cc_final: 0.8358 (mt) outliers start: 39 outliers final: 21 residues processed: 206 average time/residue: 1.3332 time to fit residues: 296.1140 Evaluate side-chains 199 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 365 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 135 optimal weight: 0.4980 chunk 117 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 410 GLN B 222 ASN B 410 GLN C 222 ASN C 410 GLN D 222 ASN D 410 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12208 Z= 0.256 Angle : 0.588 8.493 16584 Z= 0.296 Chirality : 0.038 0.135 2052 Planarity : 0.004 0.038 1992 Dihedral : 4.069 19.054 1856 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.65 % Allowed : 17.05 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.22), residues: 1500 helix: 2.45 (0.14), residues: 1228 sheet: -4.35 (0.55), residues: 44 loop : -3.17 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.004 0.001 HIS B 22 PHE 0.016 0.001 PHE A 205 TYR 0.017 0.001 TYR C 124 ARG 0.004 0.000 ARG A 306 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 170 time to evaluate : 1.428 Fit side-chains REVERT: A 193 TRP cc_start: 0.9510 (OUTLIER) cc_final: 0.7198 (m100) REVERT: A 365 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8581 (t) REVERT: B 193 TRP cc_start: 0.9507 (OUTLIER) cc_final: 0.7199 (m100) REVERT: B 365 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8580 (t) REVERT: B 389 LEU cc_start: 0.8664 (mt) cc_final: 0.8451 (mt) REVERT: C 193 TRP cc_start: 0.9507 (OUTLIER) cc_final: 0.7199 (m100) REVERT: C 365 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8578 (t) REVERT: D 193 TRP cc_start: 0.9507 (OUTLIER) cc_final: 0.7195 (m100) REVERT: D 365 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8580 (t) REVERT: D 389 LEU cc_start: 0.8664 (mt) cc_final: 0.8461 (mt) outliers start: 35 outliers final: 24 residues processed: 201 average time/residue: 1.3855 time to fit residues: 300.4655 Evaluate side-chains 198 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 166 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 420 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.0870 chunk 117 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN B 222 ASN B 410 GLN C 410 GLN D 222 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.146388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.114208 restraints weight = 20902.071| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.41 r_work: 0.3092 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12208 Z= 0.228 Angle : 0.610 13.782 16584 Z= 0.300 Chirality : 0.037 0.137 2052 Planarity : 0.004 0.038 1992 Dihedral : 4.056 18.534 1856 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.73 % Allowed : 18.03 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.22), residues: 1500 helix: 2.47 (0.14), residues: 1228 sheet: -4.35 (0.55), residues: 44 loop : -3.17 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 193 HIS 0.003 0.001 HIS B 22 PHE 0.014 0.001 PHE B 203 TYR 0.019 0.001 TYR D 124 ARG 0.005 0.000 ARG B 306 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4823.98 seconds wall clock time: 91 minutes 47.63 seconds (5507.63 seconds total)