Starting phenix.real_space_refine on Sun Feb 18 11:07:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b64_15862/02_2024/8b64_15862_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b64_15862/02_2024/8b64_15862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.589 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b64_15862/02_2024/8b64_15862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b64_15862/02_2024/8b64_15862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b64_15862/02_2024/8b64_15862_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b64_15862/02_2024/8b64_15862_updated.pdb" } resolution = 2.589 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 7 5.49 5 Mg 34 5.21 5 S 82 5.16 5 C 15257 2.51 5 N 3052 2.21 5 O 3245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21678 Number of models: 1 Model: "" Number of chains: 66 Chain: "a" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "e" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 445 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "D" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "b" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 445 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "A" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "E" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "X" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 490 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 5, 'TRANS': 57} Chain: "L" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2227 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 267} Chain: "M" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2422 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 13, 'TRANS': 290} Chain: "H" Number of atoms: 1943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1943 Classifications: {'peptide': 245} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 224} Chain: "d" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 445 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "B" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "t" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 342 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "S" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "T" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "s" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 342 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "U" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 195 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "u" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 309 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "r" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 342 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "O" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "R" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 303 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "o" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 411 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "n" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 445 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "K" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 339 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "N" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "k" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 437 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "j" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 445 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "I" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "J" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 339 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "i" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 437 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "g" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 445 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "F" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "G" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "f" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 445 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "a" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'SPO:plan-5': 1} Unresolved non-hydrogen planarities: 2 Chain: "b" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 174 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 112 Unusual residues: {'SPO': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'SPO:plan-5': 2} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 246 Unusual residues: {'3PE': 1, 'BCL': 1, 'BPH': 1, 'U10': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'U10:plan-8': 3, 'U10:plan-9': 3, 'U10:plan-3': 1, 'U10:plan-4': 2, 'U10:plan-5': 2, 'U10:plan-6': 3, 'U10:plan-7': 3, 'U10:plan-10': 3, 'U10:plan-11': 3} Unresolved non-hydrogen planarities: 92 Chain: "M" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 456 Unusual residues: {' FE': 1, '3PE': 2, 'BCL': 3, 'BPH': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "d" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'3PE': 2, 'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'SPO:plan-5': 1} Unresolved non-hydrogen planarities: 2 Chain: "t" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "S" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'SPO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'SPO:plan-5': 1} Unresolved non-hydrogen planarities: 2 Chain: "T" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "s" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 2} Unresolved non-hydrogen planarities: 12 Chain: "U" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 2} Unresolved non-hydrogen planarities: 12 Chain: "r" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 139 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "O" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'SPO:plan-5': 1} Unresolved non-hydrogen planarities: 2 Chain: "R" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'SPO:plan-5': 1} Unresolved non-hydrogen planarities: 2 Chain: "o" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "n" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 136 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'SPO:plan-5': 2} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'SPO:plan-5': 1} Unresolved non-hydrogen planarities: 2 Chain: "J" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'SPO:plan-5': 1} Unresolved non-hydrogen planarities: 2 Chain: "i" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'SPO:plan-5': 1} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.75, per 1000 atoms: 0.54 Number of scatterers: 21678 At special positions: 0 Unit cell: (101.077, 126.76, 138.359, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 1 26.01 S 82 16.00 P 7 15.00 Mg 34 11.99 O 3245 8.00 N 3052 7.00 C 15257 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=29, symmetry=0 Number of additional bonds: simple=29, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.18 Conformation dependent library (CDL) restraints added in 3.4 seconds 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4202 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 101 helices and 4 sheets defined 67.9% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'a' and resid 4 through 9 Processing helix chain 'a' and resid 13 through 37 removed outlier: 3.522A pdb=" N SER a 37 " --> pdb=" O LEU a 33 " (cutoff:3.500A) Processing helix chain 'a' and resid 39 through 41 No H-bonds generated for 'chain 'a' and resid 39 through 41' Processing helix chain 'e' and resid 4 through 9 Processing helix chain 'e' and resid 13 through 37 Processing helix chain 'e' and resid 43 through 51 Processing helix chain 'D' and resid 14 through 45 Processing helix chain 'b' and resid 4 through 9 Processing helix chain 'b' and resid 13 through 37 Processing helix chain 'b' and resid 43 through 51 Processing helix chain 'A' and resid 14 through 45 Processing helix chain 'E' and resid 14 through 45 Processing helix chain 'X' and resid 15 through 53 Proline residue: X 36 - end of helix Processing helix chain 'X' and resid 56 through 59 removed outlier: 3.511A pdb=" N HIS X 59 " --> pdb=" O GLU X 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 56 through 59' Processing helix chain 'L' and resid 7 through 9 No H-bonds generated for 'chain 'L' and resid 7 through 9' Processing helix chain 'L' and resid 32 through 56 Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'L' and resid 84 through 111 Processing helix chain 'L' and resid 116 through 132 Processing helix chain 'L' and resid 134 through 139 Processing helix chain 'L' and resid 142 through 144 No H-bonds generated for 'chain 'L' and resid 142 through 144' Processing helix chain 'L' and resid 152 through 164 removed outlier: 4.173A pdb=" N TYR L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 169 No H-bonds generated for 'chain 'L' and resid 167 through 169' Processing helix chain 'L' and resid 171 through 198 Processing helix chain 'L' and resid 209 through 220 Processing helix chain 'L' and resid 226 through 250 Processing helix chain 'L' and resid 259 through 268 removed outlier: 4.208A pdb=" N TYR L 264 " --> pdb=" O SER L 260 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N TRP L 265 " --> pdb=" O ASP L 261 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N TRP L 266 " --> pdb=" O TRP L 262 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL L 267 " --> pdb=" O TRP L 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 273 No H-bonds generated for 'chain 'L' and resid 270 through 273' Processing helix chain 'M' and resid 26 through 28 No H-bonds generated for 'chain 'M' and resid 26 through 28' Processing helix chain 'M' and resid 36 through 39 Processing helix chain 'M' and resid 52 through 76 removed outlier: 3.705A pdb=" N THR M 56 " --> pdb=" O GLY M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 86 Processing helix chain 'M' and resid 98 through 100 No H-bonds generated for 'chain 'M' and resid 98 through 100' Processing helix chain 'M' and resid 107 through 109 No H-bonds generated for 'chain 'M' and resid 107 through 109' Processing helix chain 'M' and resid 111 through 137 Processing helix chain 'M' and resid 143 through 159 removed outlier: 3.546A pdb=" N SER M 150 " --> pdb=" O TRP M 146 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA M 151 " --> pdb=" O ALA M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 166 Processing helix chain 'M' and resid 169 through 171 No H-bonds generated for 'chain 'M' and resid 169 through 171' Processing helix chain 'M' and resid 177 through 190 removed outlier: 3.901A pdb=" N LEU M 181 " --> pdb=" O ILE M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 196 No H-bonds generated for 'chain 'M' and resid 194 through 196' Processing helix chain 'M' and resid 198 through 223 Processing helix chain 'M' and resid 225 through 227 No H-bonds generated for 'chain 'M' and resid 225 through 227' Processing helix chain 'M' and resid 232 through 237 Processing helix chain 'M' and resid 241 through 254 Processing helix chain 'M' and resid 262 through 284 removed outlier: 3.905A pdb=" N VAL M 274 " --> pdb=" O MET M 270 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR M 275 " --> pdb=" O ALA M 271 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE M 280 " --> pdb=" O LEU M 276 " (cutoff:3.500A) Processing helix chain 'M' and resid 292 through 299 Processing helix chain 'H' and resid 12 through 35 Processing helix chain 'H' and resid 77 through 82 Processing helix chain 'H' and resid 107 through 110 No H-bonds generated for 'chain 'H' and resid 107 through 110' Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 137 through 139 No H-bonds generated for 'chain 'H' and resid 137 through 139' Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 212 through 217 removed outlier: 4.304A pdb=" N ASP H 216 " --> pdb=" O SER H 212 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR H 217 " --> pdb=" O ASP H 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 212 through 217' Processing helix chain 'H' and resid 229 through 242 removed outlier: 3.684A pdb=" N GLY H 242 " --> pdb=" O TYR H 238 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 9 Processing helix chain 'd' and resid 13 through 37 Processing helix chain 'd' and resid 43 through 51 Processing helix chain 'B' and resid 14 through 45 Processing helix chain 't' and resid 13 through 37 Processing helix chain 't' and resid 39 through 41 No H-bonds generated for 'chain 't' and resid 39 through 41' Processing helix chain 't' and resid 43 through 51 Processing helix chain 'S' and resid 14 through 45 Processing helix chain 'T' and resid 14 through 46 Processing helix chain 's' and resid 13 through 37 Processing helix chain 's' and resid 43 through 51 Processing helix chain 'U' and resid 21 through 44 Processing helix chain 'u' and resid 16 through 37 Processing helix chain 'u' and resid 43 through 50 Processing helix chain 'r' and resid 13 through 37 Processing helix chain 'r' and resid 43 through 51 Processing helix chain 'O' and resid 14 through 45 Processing helix chain 'R' and resid 14 through 45 Processing helix chain 'o' and resid 6 through 10 Processing helix chain 'o' and resid 13 through 37 Processing helix chain 'o' and resid 43 through 51 Processing helix chain 'n' and resid 3 through 9 Processing helix chain 'n' and resid 13 through 37 Processing helix chain 'n' and resid 43 through 51 Processing helix chain 'K' and resid 14 through 45 Processing helix chain 'N' and resid 14 through 45 Processing helix chain 'k' and resid 4 through 9 Processing helix chain 'k' and resid 13 through 36 Processing helix chain 'k' and resid 43 through 51 Processing helix chain 'j' and resid 4 through 9 Processing helix chain 'j' and resid 13 through 37 Processing helix chain 'j' and resid 43 through 51 Processing helix chain 'I' and resid 14 through 45 Processing helix chain 'J' and resid 14 through 45 Processing helix chain 'i' and resid 4 through 9 Processing helix chain 'i' and resid 13 through 37 Processing helix chain 'i' and resid 43 through 50 Processing helix chain 'g' and resid 4 through 9 Processing helix chain 'g' and resid 13 through 37 Processing helix chain 'g' and resid 43 through 51 Processing helix chain 'F' and resid 14 through 45 Processing helix chain 'G' and resid 14 through 45 Processing helix chain 'f' and resid 4 through 9 Processing helix chain 'f' and resid 13 through 37 Processing helix chain 'f' and resid 39 through 41 No H-bonds generated for 'chain 'f' and resid 39 through 41' Processing helix chain 'f' and resid 43 through 51 Processing sheet with id= A, first strand: chain 'H' and resid 63 through 65 Processing sheet with id= B, first strand: chain 'H' and resid 90 through 92 Processing sheet with id= C, first strand: chain 'H' and resid 134 through 136 removed outlier: 6.895A pdb=" N GLU H 182 " --> pdb=" O VAL H 167 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N MET H 169 " --> pdb=" O TYR H 180 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR H 180 " --> pdb=" O MET H 169 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 204 through 206 removed outlier: 3.910A pdb=" N GLY H 164 " --> pdb=" O VAL H 155 " (cutoff:3.500A) 1146 hydrogen bonds defined for protein. 3336 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: 5.89 Time building geometry restraints manager: 9.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.37: 6366 1.37 - 1.57: 15420 1.57 - 1.77: 431 1.77 - 1.98: 159 1.98 - 2.18: 136 Bond restraints: 22512 Sorted by residual: bond pdb=" C4 U10 L 305 " pdb=" O4 U10 L 305 " ideal model delta sigma weight residual 1.230 1.421 -0.191 2.00e-02 2.50e+03 9.10e+01 bond pdb=" C3 U10 L 305 " pdb=" O3 U10 L 305 " ideal model delta sigma weight residual 1.230 1.418 -0.188 2.00e-02 2.50e+03 8.80e+01 bond pdb=" C23 SPO M 404 " pdb=" C25 SPO M 404 " ideal model delta sigma weight residual 1.448 1.636 -0.188 2.00e-02 2.50e+03 8.80e+01 bond pdb=" C3 U10 M 403 " pdb=" O3 U10 M 403 " ideal model delta sigma weight residual 1.230 1.417 -0.187 2.00e-02 2.50e+03 8.78e+01 bond pdb=" C3 U10 L 303 " pdb=" O3 U10 L 303 " ideal model delta sigma weight residual 1.230 1.415 -0.185 2.00e-02 2.50e+03 8.57e+01 ... (remaining 22507 not shown) Histogram of bond angle deviations from ideal: 62.56 - 84.03: 41 84.03 - 105.50: 1173 105.50 - 126.96: 28422 126.96 - 148.43: 1182 148.43 - 169.90: 178 Bond angle restraints: 30996 Sorted by residual: angle pdb=" C34 SPO M 404 " pdb=" C33 SPO M 404 " pdb=" C35 SPO M 404 " ideal model delta sigma weight residual 115.46 62.56 52.90 3.00e+00 1.11e-01 3.11e+02 angle pdb=" C34 SPO d 102 " pdb=" C33 SPO d 102 " pdb=" C35 SPO d 102 " ideal model delta sigma weight residual 115.46 63.19 52.27 3.00e+00 1.11e-01 3.04e+02 angle pdb=" C10 U10 L 305 " pdb=" C9 U10 L 305 " pdb=" C11 U10 L 305 " ideal model delta sigma weight residual 120.00 67.77 52.23 3.00e+00 1.11e-01 3.03e+02 angle pdb=" C25 U10 L 303 " pdb=" C24 U10 L 303 " pdb=" C26 U10 L 303 " ideal model delta sigma weight residual 120.00 67.80 52.20 3.00e+00 1.11e-01 3.03e+02 angle pdb=" C34 SPO i 102 " pdb=" C33 SPO i 102 " pdb=" C35 SPO i 102 " ideal model delta sigma weight residual 115.46 63.31 52.15 3.00e+00 1.11e-01 3.02e+02 ... (remaining 30991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 11426 35.99 - 71.97: 417 71.97 - 107.96: 100 107.96 - 143.94: 4 143.94 - 179.93: 26 Dihedral angle restraints: 11973 sinusoidal: 5480 harmonic: 6493 Sorted by residual: dihedral pdb=" C1 BCL b 102 " pdb=" C2 BCL b 102 " pdb=" C3 BCL b 102 " pdb=" C5 BCL b 102 " ideal model delta sinusoidal sigma weight residual -180.00 -0.07 -179.93 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL a 100 " pdb=" C2 BCL a 100 " pdb=" C3 BCL a 100 " pdb=" C5 BCL a 100 " ideal model delta sinusoidal sigma weight residual -180.00 -0.08 -179.92 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL f 101 " pdb=" C2 BCL f 101 " pdb=" C3 BCL f 101 " pdb=" C5 BCL f 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.09 -179.91 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 11970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2432 0.043 - 0.085: 580 0.085 - 0.128: 91 0.128 - 0.171: 10 0.171 - 0.214: 2 Chirality restraints: 3115 Sorted by residual: chirality pdb=" C2C BPH L 302 " pdb=" C1C BPH L 302 " pdb=" C3C BPH L 302 " pdb=" CMC BPH L 302 " both_signs ideal model delta sigma weight residual False -2.81 -2.60 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C2C BPH M 408 " pdb=" C1C BPH M 408 " pdb=" C3C BPH M 408 " pdb=" CMC BPH M 408 " both_signs ideal model delta sigma weight residual False -2.81 -2.60 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C8 BPH M 408 " pdb=" C10 BPH M 408 " pdb=" C7 BPH M 408 " pdb=" C9 BPH M 408 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.98e-01 ... (remaining 3112 not shown) Planarity restraints: 3837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BPH M 408 " 0.015 2.00e-02 2.50e+03 5.06e-02 5.75e+01 pdb=" C1D BPH M 408 " 0.015 2.00e-02 2.50e+03 pdb=" C2D BPH M 408 " -0.026 2.00e-02 2.50e+03 pdb=" C3D BPH M 408 " -0.046 2.00e-02 2.50e+03 pdb=" C4D BPH M 408 " -0.023 2.00e-02 2.50e+03 pdb=" CAD BPH M 408 " 0.113 2.00e-02 2.50e+03 pdb=" CHA BPH M 408 " -0.048 2.00e-02 2.50e+03 pdb=" CHD BPH M 408 " 0.047 2.00e-02 2.50e+03 pdb=" CMD BPH M 408 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BPH L 302 " -0.016 2.00e-02 2.50e+03 3.97e-02 3.54e+01 pdb=" C1D BPH L 302 " -0.009 2.00e-02 2.50e+03 pdb=" C2D BPH L 302 " 0.021 2.00e-02 2.50e+03 pdb=" C3D BPH L 302 " 0.040 2.00e-02 2.50e+03 pdb=" C4D BPH L 302 " 0.020 2.00e-02 2.50e+03 pdb=" CAD BPH L 302 " -0.089 2.00e-02 2.50e+03 pdb=" CHA BPH L 302 " 0.036 2.00e-02 2.50e+03 pdb=" CHD BPH L 302 " -0.035 2.00e-02 2.50e+03 pdb=" CMD BPH L 302 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BPH M 408 " -0.001 2.00e-02 2.50e+03 1.48e-02 4.91e+00 pdb=" C1B BPH M 408 " 0.010 2.00e-02 2.50e+03 pdb=" C2B BPH M 408 " -0.004 2.00e-02 2.50e+03 pdb=" C3B BPH M 408 " 0.001 2.00e-02 2.50e+03 pdb=" C4B BPH M 408 " -0.012 2.00e-02 2.50e+03 pdb=" CAB BPH M 408 " 0.027 2.00e-02 2.50e+03 pdb=" CHB BPH M 408 " 0.015 2.00e-02 2.50e+03 pdb=" CHC BPH M 408 " -0.011 2.00e-02 2.50e+03 pdb=" CMB BPH M 408 " -0.025 2.00e-02 2.50e+03 ... (remaining 3834 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 146 2.56 - 3.15: 15777 3.15 - 3.73: 35991 3.73 - 4.32: 51985 4.32 - 4.90: 84327 Nonbonded interactions: 188226 Sorted by model distance: nonbonded pdb=" OE2 GLU M 232 " pdb="FE FE M 402 " model vdw 1.980 2.260 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE M 402 " model vdw 2.082 2.340 nonbonded pdb=" NE2 HIS M 217 " pdb="FE FE M 402 " model vdw 2.106 2.340 nonbonded pdb=" OH TYR X 65 " pdb=" O ALA L 145 " model vdw 2.211 2.440 nonbonded pdb=" OH TYR L 255 " pdb=" O LEU L 258 " model vdw 2.220 2.440 ... (remaining 188221 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 8 through 49) selection = (chain 'B' and resid 8 through 49) selection = (chain 'D' and resid 8 through 49) selection = (chain 'E' and resid 8 through 49) selection = (chain 'F' and resid 8 through 49) selection = (chain 'G' and resid 8 through 49) selection = (chain 'I' and resid 8 through 49) selection = (chain 'J' and resid 8 through 49) selection = (chain 'K' and resid 8 through 49) selection = (chain 'N' and resid 8 through 49) selection = (chain 'O' and resid 8 through 49) } ncs_group { reference = (chain 'R' and resid 13 through 49) selection = (chain 'S' and resid 13 through 49) selection = (chain 'T' and resid 13 through 49) } ncs_group { reference = (chain 'a' and resid 5 through 44) selection = (chain 'o' and resid 5 through 44) } ncs_group { reference = (chain 'b' and (resid 2 through 54 or resid 101)) selection = (chain 'd' and (resid 2 through 54 or resid 101)) selection = (chain 'e' and (resid 2 through 54 or resid 101)) selection = (chain 'f' and (resid 2 through 54 or resid 101)) selection = (chain 'g' and (resid 2 through 54 or resid 101)) selection = (chain 'i' and (resid 2 through 54 or resid 101)) selection = (chain 'j' and (resid 2 through 54 or resid 101)) selection = (chain 'k' and (resid 2 through 54 or resid 101)) selection = (chain 'n' and (resid 2 through 54 or resid 101)) } ncs_group { reference = (chain 'r' and (resid 12 through 54 or (resid 101 and (name NB or name ND or nam \ e C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or \ name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4 \ B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or nam \ e CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or \ name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CM \ C or name CMD or name NA or name NC or name O1A or name O1D or name O2A or name \ O2D or name OBB or name OBD or name MG )))) selection = (chain 's' and (resid 12 through 54 or resid 101)) selection = (chain 't' and (resid 12 through 54 or resid 101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 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: 0.020 Extract box with map and model: 7.250 Check model and map are aligned: 0.310 Set scattering table: 0.210 Process input model: 55.980 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.190 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:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 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 : 0.020 0.191 22512 Z= 1.073 Angle : 4.456 52.896 30996 Z= 1.492 Chirality : 0.036 0.214 3115 Planarity : 0.004 0.051 3837 Dihedral : 21.085 179.931 7771 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.19 % Allowed : 3.90 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 3.50 (0.18), residues: 2181 helix: 3.09 (0.12), residues: 1485 sheet: -0.67 (0.92), residues: 32 loop : 0.67 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 185 HIS 0.006 0.001 HIS M 180 PHE 0.014 0.001 PHE L 146 TYR 0.015 0.001 TYR M 301 ARG 0.002 0.000 ARG L 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 283 time to evaluate : 2.230 Fit side-chains REVERT: a 6 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8598 (mtpp) REVERT: b 53 TYR cc_start: 0.6444 (OUTLIER) cc_final: 0.4398 (p90) REVERT: X 6 LYS cc_start: 0.7956 (mttm) cc_final: 0.7746 (mttm) REVERT: X 9 ASP cc_start: 0.7555 (t0) cc_final: 0.7277 (t70) REVERT: X 24 ARG cc_start: 0.8412 (mtt-85) cc_final: 0.8188 (mtt90) REVERT: M 166 MET cc_start: 0.9164 (mmm) cc_final: 0.8910 (mmm) REVERT: H 91 GLU cc_start: 0.8050 (tt0) cc_final: 0.7830 (tt0) REVERT: B 9 PHE cc_start: 0.9076 (m-80) cc_final: 0.8873 (m-80) REVERT: r 31 ILE cc_start: 0.7948 (mt) cc_final: 0.7707 (mt) outliers start: 22 outliers final: 8 residues processed: 300 average time/residue: 1.2313 time to fit residues: 423.4972 Evaluate side-chains 264 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 255 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 35 PHE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain d residue 1 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 101 optimal weight: 0.0870 chunk 123 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 42 ASN H 135 GLN H 176 GLN ** r 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 16 GLN o 20 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.0603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22512 Z= 0.172 Angle : 1.535 44.450 30996 Z= 0.530 Chirality : 0.035 0.164 3115 Planarity : 0.004 0.071 3837 Dihedral : 25.567 179.995 3967 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.06 % Allowed : 7.04 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 3.56 (0.17), residues: 2181 helix: 3.10 (0.12), residues: 1494 sheet: -0.38 (0.94), residues: 32 loop : 0.75 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 155 HIS 0.013 0.001 HIS L 153 PHE 0.014 0.001 PHE L 146 TYR 0.014 0.001 TYR M 301 ARG 0.006 0.000 ARG f 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 259 time to evaluate : 2.044 Fit side-chains REVERT: a 6 LYS cc_start: 0.8814 (mtpt) cc_final: 0.8581 (mtpp) REVERT: b 53 TYR cc_start: 0.6484 (OUTLIER) cc_final: 0.4189 (p90) REVERT: X 24 ARG cc_start: 0.8423 (mtt-85) cc_final: 0.8189 (mtt90) REVERT: M 166 MET cc_start: 0.9163 (mmm) cc_final: 0.8899 (mmm) REVERT: d 1 MET cc_start: 0.6495 (OUTLIER) cc_final: 0.6253 (ttm) REVERT: B 9 PHE cc_start: 0.9076 (m-80) cc_final: 0.8871 (m-80) REVERT: B 40 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8522 (tp) REVERT: r 31 ILE cc_start: 0.7908 (mt) cc_final: 0.7670 (mt) REVERT: I 40 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8442 (mt) outliers start: 38 outliers final: 20 residues processed: 275 average time/residue: 1.2030 time to fit residues: 380.5676 Evaluate side-chains 278 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 254 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain E residue 43 MET Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 35 PHE Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain G residue 43 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 208 optimal weight: 0.8980 chunk 171 optimal weight: 9.9990 chunk 191 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 154 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 42 ASN H 135 GLN H 176 GLN ** r 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22512 Z= 0.207 Angle : 1.320 43.919 30996 Z= 0.464 Chirality : 0.037 0.172 3115 Planarity : 0.004 0.038 3837 Dihedral : 24.878 179.998 3967 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.22 % Allowed : 7.26 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 3.44 (0.17), residues: 2181 helix: 3.02 (0.12), residues: 1491 sheet: -0.42 (0.93), residues: 32 loop : 0.71 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 250 HIS 0.012 0.001 HIS L 153 PHE 0.016 0.001 PHE L 146 TYR 0.014 0.001 TYR b 53 ARG 0.008 0.001 ARG f 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 257 time to evaluate : 2.104 Fit side-chains REVERT: e 3 LYS cc_start: 0.8259 (mttt) cc_final: 0.7988 (mttm) REVERT: b 53 TYR cc_start: 0.6567 (OUTLIER) cc_final: 0.3971 (p90) REVERT: E 7 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6292 (tp) REVERT: X 6 LYS cc_start: 0.8082 (mttm) cc_final: 0.7489 (mmtm) REVERT: X 24 ARG cc_start: 0.8386 (mtt-85) cc_final: 0.8168 (mtt90) REVERT: X 56 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: M 166 MET cc_start: 0.9180 (mmm) cc_final: 0.8877 (mmm) REVERT: d 1 MET cc_start: 0.6563 (OUTLIER) cc_final: 0.6314 (ttm) REVERT: B 9 PHE cc_start: 0.9089 (m-80) cc_final: 0.8866 (m-80) REVERT: B 15 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6352 (pp20) REVERT: B 40 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8490 (tp) REVERT: r 31 ILE cc_start: 0.7983 (mt) cc_final: 0.7747 (mt) REVERT: I 40 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8423 (mt) outliers start: 41 outliers final: 17 residues processed: 282 average time/residue: 1.2895 time to fit residues: 416.3690 Evaluate side-chains 275 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 251 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 43 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 100 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 129 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 chunk 204 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 42 ASN E 18 GLN H 135 GLN H 176 GLN ** r 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22512 Z= 0.155 Angle : 1.218 44.209 30996 Z= 0.429 Chirality : 0.035 0.158 3115 Planarity : 0.003 0.034 3837 Dihedral : 23.962 179.978 3965 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.17 % Allowed : 8.12 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 3.56 (0.17), residues: 2181 helix: 3.11 (0.12), residues: 1490 sheet: -0.18 (0.96), residues: 32 loop : 0.75 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 155 HIS 0.010 0.001 HIS L 153 PHE 0.015 0.001 PHE L 146 TYR 0.013 0.001 TYR M 301 ARG 0.008 0.000 ARG f 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 258 time to evaluate : 2.096 Fit side-chains revert: symmetry clash REVERT: a 12 ASP cc_start: 0.8737 (t70) cc_final: 0.8316 (t0) REVERT: e 3 LYS cc_start: 0.8260 (mttt) cc_final: 0.7990 (mttm) REVERT: b 53 TYR cc_start: 0.6436 (OUTLIER) cc_final: 0.3883 (p90) REVERT: X 6 LYS cc_start: 0.8099 (mttm) cc_final: 0.7506 (mmtm) REVERT: X 24 ARG cc_start: 0.8383 (mtt-85) cc_final: 0.8157 (mtt90) REVERT: X 56 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7740 (tm-30) REVERT: M 166 MET cc_start: 0.9179 (mmm) cc_final: 0.8917 (mmm) REVERT: B 9 PHE cc_start: 0.9050 (m-80) cc_final: 0.8818 (m-80) REVERT: B 15 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6251 (pp20) REVERT: B 40 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8480 (tp) REVERT: r 31 ILE cc_start: 0.7928 (mt) cc_final: 0.7696 (mt) REVERT: j 33 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8615 (tp) REVERT: I 40 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8405 (mt) outliers start: 40 outliers final: 17 residues processed: 278 average time/residue: 1.2200 time to fit residues: 390.1367 Evaluate side-chains 278 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 255 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 43 MET Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain i residue 3 LYS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 152 optimal weight: 30.0000 chunk 84 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 42 ASN E 18 GLN H 135 GLN H 176 GLN H 208 ASN S 21 HIS ** r 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 22512 Z= 0.422 Angle : 1.305 44.667 30996 Z= 0.480 Chirality : 0.047 0.280 3115 Planarity : 0.005 0.063 3837 Dihedral : 23.712 179.989 3962 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.76 % Allowed : 7.58 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 2.74 (0.17), residues: 2181 helix: 2.47 (0.12), residues: 1485 sheet: -0.69 (1.11), residues: 22 loop : 0.48 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP M 250 HIS 0.013 0.002 HIS L 153 PHE 0.023 0.003 PHE L 146 TYR 0.021 0.003 TYR L 164 ARG 0.008 0.001 ARG F 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 255 time to evaluate : 2.380 Fit side-chains revert: symmetry clash REVERT: e 3 LYS cc_start: 0.8417 (mttt) cc_final: 0.8143 (mttm) REVERT: b 53 TYR cc_start: 0.6908 (OUTLIER) cc_final: 0.4455 (p90) REVERT: b 54 VAL cc_start: 0.6119 (OUTLIER) cc_final: 0.5840 (p) REVERT: E 7 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6261 (tp) REVERT: X 6 LYS cc_start: 0.8081 (mttm) cc_final: 0.7499 (mmtm) REVERT: H 38 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7885 (mm-30) REVERT: H 70 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7872 (mtp180) REVERT: B 40 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8484 (tp) REVERT: j 33 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8632 (tp) REVERT: I 40 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8497 (mt) REVERT: J 9 PHE cc_start: 0.8799 (m-80) cc_final: 0.8596 (m-80) outliers start: 51 outliers final: 22 residues processed: 286 average time/residue: 1.3198 time to fit residues: 428.7583 Evaluate side-chains 278 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 248 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain X residue 53 MET Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain o residue 48 THR Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 43 MET Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain i residue 3 LYS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 43 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 170 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 42 ASN E 18 GLN H 135 GLN H 176 GLN ** r 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22512 Z= 0.151 Angle : 1.081 43.352 30996 Z= 0.387 Chirality : 0.036 0.157 3115 Planarity : 0.003 0.037 3837 Dihedral : 22.715 179.997 3960 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.06 % Allowed : 8.61 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 3.28 (0.17), residues: 2181 helix: 2.90 (0.12), residues: 1487 sheet: -0.40 (0.91), residues: 32 loop : 0.63 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 65 HIS 0.010 0.001 HIS L 153 PHE 0.017 0.001 PHE L 146 TYR 0.015 0.001 TYR M 301 ARG 0.007 0.000 ARG f 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 259 time to evaluate : 2.329 Fit side-chains revert: symmetry clash REVERT: e 3 LYS cc_start: 0.8343 (mttt) cc_final: 0.8073 (mttm) REVERT: b 53 TYR cc_start: 0.6562 (OUTLIER) cc_final: 0.4293 (p90) REVERT: b 54 VAL cc_start: 0.5878 (OUTLIER) cc_final: 0.5637 (p) REVERT: X 6 LYS cc_start: 0.8182 (mttm) cc_final: 0.7559 (mmtm) REVERT: X 56 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: B 40 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8462 (tp) REVERT: O 25 MET cc_start: 0.7736 (mmm) cc_final: 0.6995 (mmm) REVERT: I 40 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8439 (mt) outliers start: 38 outliers final: 21 residues processed: 282 average time/residue: 1.2754 time to fit residues: 411.8935 Evaluate side-chains 276 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 250 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 43 MET Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain i residue 3 LYS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 43 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 204 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 42 ASN E 18 GLN H 135 GLN H 176 GLN ** r 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 22512 Z= 0.455 Angle : 1.264 42.925 30996 Z= 0.471 Chirality : 0.049 0.302 3115 Planarity : 0.005 0.065 3837 Dihedral : 22.941 179.989 3960 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.38 % Allowed : 8.55 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 2.57 (0.17), residues: 2181 helix: 2.35 (0.12), residues: 1487 sheet: -0.81 (1.09), residues: 22 loop : 0.40 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP M 250 HIS 0.017 0.002 HIS L 153 PHE 0.023 0.003 PHE L 146 TYR 0.023 0.003 TYR b 53 ARG 0.009 0.001 ARG F 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 247 time to evaluate : 2.180 Fit side-chains revert: symmetry clash REVERT: e 3 LYS cc_start: 0.8475 (mttt) cc_final: 0.8201 (mttm) REVERT: b 53 TYR cc_start: 0.6990 (OUTLIER) cc_final: 0.5069 (p90) REVERT: b 54 VAL cc_start: 0.6193 (OUTLIER) cc_final: 0.5948 (p) REVERT: E 7 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6059 (tp) REVERT: X 6 LYS cc_start: 0.8146 (mttm) cc_final: 0.7581 (mmtm) REVERT: H 70 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7887 (mtp180) REVERT: B 40 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8490 (tp) REVERT: I 19 GLU cc_start: 0.7449 (tt0) cc_final: 0.7236 (tt0) REVERT: I 40 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8503 (mt) outliers start: 44 outliers final: 20 residues processed: 269 average time/residue: 1.3356 time to fit residues: 408.1810 Evaluate side-chains 270 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 244 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain i residue 3 LYS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 43 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 chunk 129 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 185 optimal weight: 9.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 42 ASN E 18 GLN H 135 GLN H 176 GLN ** r 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22512 Z= 0.151 Angle : 1.074 43.368 30996 Z= 0.384 Chirality : 0.036 0.182 3115 Planarity : 0.003 0.039 3837 Dihedral : 22.052 179.990 3960 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 1.30 % Allowed : 9.91 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 3.23 (0.17), residues: 2181 helix: 2.86 (0.12), residues: 1489 sheet: -0.42 (0.91), residues: 32 loop : 0.63 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP n 8 HIS 0.009 0.001 HIS L 153 PHE 0.019 0.001 PHE L 146 TYR 0.014 0.001 TYR M 301 ARG 0.007 0.000 ARG k 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 253 time to evaluate : 2.138 Fit side-chains REVERT: e 3 LYS cc_start: 0.8349 (mttt) cc_final: 0.8072 (mttm) REVERT: b 53 TYR cc_start: 0.6524 (OUTLIER) cc_final: 0.4544 (p90) REVERT: E 7 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6085 (tp) REVERT: X 6 LYS cc_start: 0.8169 (mttm) cc_final: 0.7543 (mmtm) REVERT: X 56 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7803 (tm-30) REVERT: r 31 ILE cc_start: 0.7926 (mt) cc_final: 0.7679 (mt) REVERT: O 25 MET cc_start: 0.7759 (mmm) cc_final: 0.7020 (mmm) REVERT: I 40 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8439 (mt) outliers start: 24 outliers final: 16 residues processed: 270 average time/residue: 1.2513 time to fit residues: 387.9364 Evaluate side-chains 272 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 252 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 43 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 190 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 189 optimal weight: 0.8980 chunk 125 optimal weight: 20.0000 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 42 ASN E 18 GLN M 43 ASN H 135 GLN H 176 GLN ** r 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 22512 Z= 0.320 Angle : 1.169 43.049 30996 Z= 0.430 Chirality : 0.043 0.234 3115 Planarity : 0.005 0.055 3837 Dihedral : 22.287 179.994 3959 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.84 % Allowed : 9.42 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 2.92 (0.17), residues: 2181 helix: 2.64 (0.12), residues: 1480 sheet: -0.50 (1.13), residues: 22 loop : 0.49 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 250 HIS 0.014 0.002 HIS L 153 PHE 0.021 0.002 PHE L 146 TYR 0.020 0.002 TYR b 53 ARG 0.008 0.001 ARG f 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 252 time to evaluate : 2.150 Fit side-chains revert: symmetry clash REVERT: e 3 LYS cc_start: 0.8446 (mttt) cc_final: 0.8175 (mttm) REVERT: b 53 TYR cc_start: 0.6853 (OUTLIER) cc_final: 0.4702 (p90) REVERT: E 7 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.5949 (tp) REVERT: X 6 LYS cc_start: 0.8080 (mttm) cc_final: 0.7502 (mmtm) REVERT: B 9 PHE cc_start: 0.9079 (m-80) cc_final: 0.8857 (m-80) REVERT: B 40 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8487 (tp) REVERT: O 25 MET cc_start: 0.7784 (mmm) cc_final: 0.7144 (mmm) REVERT: I 19 GLU cc_start: 0.7365 (tt0) cc_final: 0.7148 (tt0) REVERT: I 40 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8469 (mt) outliers start: 34 outliers final: 18 residues processed: 273 average time/residue: 1.3347 time to fit residues: 414.3564 Evaluate side-chains 270 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 248 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain i residue 3 LYS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 43 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 168 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 42 ASN E 18 GLN H 135 GLN H 176 GLN ** r 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22512 Z= 0.256 Angle : 1.133 43.160 30996 Z= 0.413 Chirality : 0.040 0.200 3115 Planarity : 0.004 0.047 3837 Dihedral : 22.086 179.994 3959 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.41 % Allowed : 9.91 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 2.94 (0.17), residues: 2181 helix: 2.62 (0.12), residues: 1486 sheet: -0.37 (1.14), residues: 22 loop : 0.55 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP n 8 HIS 0.014 0.001 HIS L 153 PHE 0.021 0.002 PHE L 146 TYR 0.017 0.002 TYR b 53 ARG 0.007 0.001 ARG f 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 251 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 3 LYS cc_start: 0.8452 (mttt) cc_final: 0.8174 (mttm) REVERT: E 7 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.5896 (tp) REVERT: X 6 LYS cc_start: 0.8088 (mttm) cc_final: 0.7507 (mmtm) REVERT: d 12 ASP cc_start: 0.8804 (t70) cc_final: 0.8550 (t70) REVERT: B 9 PHE cc_start: 0.9089 (m-80) cc_final: 0.8852 (m-80) REVERT: O 25 MET cc_start: 0.7780 (mmm) cc_final: 0.7105 (mmm) REVERT: I 19 GLU cc_start: 0.7339 (tt0) cc_final: 0.7111 (tt0) REVERT: I 40 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8474 (mt) outliers start: 26 outliers final: 19 residues processed: 268 average time/residue: 1.4078 time to fit residues: 429.0266 Evaluate side-chains 268 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 247 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain i residue 3 LYS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 43 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 172 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 18 GLN H 135 GLN H 176 GLN ** r 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.140809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.102284 restraints weight = 21629.887| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.43 r_work: 0.2622 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22512 Z= 0.183 Angle : 1.089 43.297 30996 Z= 0.393 Chirality : 0.037 0.174 3115 Planarity : 0.004 0.041 3837 Dihedral : 21.677 179.952 3959 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.46 % Allowed : 9.91 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 3.20 (0.17), residues: 2181 helix: 2.82 (0.12), residues: 1487 sheet: -0.08 (1.17), residues: 22 loop : 0.63 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP n 8 HIS 0.012 0.001 HIS L 153 PHE 0.019 0.001 PHE L 146 TYR 0.016 0.001 TYR a 5 ARG 0.007 0.000 ARG k 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6898.66 seconds wall clock time: 123 minutes 53.71 seconds (7433.71 seconds total)