Starting phenix.real_space_refine on Sun Feb 18 16:09:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vny_32047/02_2024/7vny_32047_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vny_32047/02_2024/7vny_32047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vny_32047/02_2024/7vny_32047.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vny_32047/02_2024/7vny_32047.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vny_32047/02_2024/7vny_32047_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vny_32047/02_2024/7vny_32047_updated.pdb" } resolution = 2.79 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= 0.015 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 13 5.49 5 Mg 32 5.21 5 S 90 5.16 5 C 15852 2.51 5 N 3120 2.21 5 O 3364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L GLU 6": "OE1" <-> "OE2" Residue "L GLU 212": "OE1" <-> "OE2" Residue "L PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 218": "OD1" <-> "OD2" Residue "M TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 100": "OE1" <-> "OE2" Residue "M GLU 173": "OE1" <-> "OE2" Residue "M ASP 184": "OD1" <-> "OD2" Residue "M GLU 236": "OE1" <-> "OE2" Residue "H PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H GLU 173": "OE1" <-> "OE2" Residue "H GLU 182": "OE1" <-> "OE2" Residue "H ASP 185": "OD1" <-> "OD2" Residue "A ASP 12": "OD1" <-> "OD2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "E TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 19": "OE1" <-> "OE2" Residue "F GLU 45": "OE1" <-> "OE2" Residue "I TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 12": "OD1" <-> "OD2" Residue "J TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 15": "OE1" <-> "OE2" Residue "N TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 45": "OE1" <-> "OE2" Residue "P TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "R PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 12": "OD1" <-> "OD2" Residue "T TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 19": "OE1" <-> "OE2" Residue "3 PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 45": "OE1" <-> "OE2" Residue "2 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 12": "OD1" <-> "OD2" 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: 22472 Number of models: 1 Model: "" Number of chains: 64 Chain: "L" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2232 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2431 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain: "H" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1875 Classifications: {'peptide': 247} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 223} Chain: "A" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "B" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "D" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "E" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "G" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "I" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "J" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "K" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "N" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "O" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "P" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "R" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "S" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "T" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "U" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "V" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "W" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "C" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "3" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "Z" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "1" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "2" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 316 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "7" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 392 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "8" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "9" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "0" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "X" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 406 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "Y" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 368 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "L" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 409 Unusual residues: {'BCL': 3, 'BPB': 1, 'PC1': 2, 'U10': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 36 Chain: "M" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 312 Unusual residues: {'BCL': 1, 'BPB': 1, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 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: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'CDL': 1, 'PC1': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'PC1:plan-2': 1, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 209 Unusual residues: {'BCL': 2, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 187 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "E" 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: "F" 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: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} 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: "J" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "N" 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: "O" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 216 Unusual residues: {'BCL': 2, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "P" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "S" 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: "T" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'SPO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 216 Unusual residues: {'BCL': 2, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "V" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 216 Unusual residues: {'BCL': 2, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "1" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 117 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "7" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "9" 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: "0" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'SPO:plan-4': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'U10': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 11.85, per 1000 atoms: 0.53 Number of scatterers: 22472 At special positions: 0 Unit cell: (138.86, 132.5, 112.36, 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 90 16.00 P 13 15.00 Mg 32 11.99 O 3364 8.00 N 3120 7.00 C 15852 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=31, symmetry=0 Number of additional bonds: simple=31, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.32 Conformation dependent library (CDL) restraints added in 3.2 seconds 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4242 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 95 helices and 5 sheets defined 65.6% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... 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 33 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 removed outlier: 3.624A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) 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: 4.057A 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 219 Processing helix chain 'L' and resid 226 through 249 Processing helix chain 'L' and resid 259 through 267 removed outlier: 4.183A pdb=" N GLN L 264 " --> pdb=" O VAL L 260 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TRP L 265 " --> pdb=" O ASP L 261 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N TRP L 266 " --> pdb=" O TRP L 262 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL L 267 " --> pdb=" O TRP L 263 " (cutoff:3.500A) 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 37 through 42 Processing helix chain 'M' and resid 54 through 77 Processing helix chain 'M' and resid 82 through 88 Processing helix chain 'M' and resid 99 through 101 No H-bonds generated for 'chain 'M' and resid 99 through 101' Processing helix chain 'M' and resid 113 through 139 Processing helix chain 'M' and resid 145 through 161 Processing helix chain 'M' and resid 163 through 168 Processing helix chain 'M' and resid 171 through 173 No H-bonds generated for 'chain 'M' and resid 171 through 173' Processing helix chain 'M' and resid 179 through 192 removed outlier: 3.910A pdb=" N LEU M 183 " --> pdb=" O ILE M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 198 No H-bonds generated for 'chain 'M' and resid 196 through 198' Processing helix chain 'M' and resid 200 through 229 removed outlier: 4.740A pdb=" N ARG M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N PHE M 229 " --> pdb=" O ALA M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 239 removed outlier: 3.614A pdb=" N ALA M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 256 Processing helix chain 'M' and resid 264 through 286 removed outlier: 3.715A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 300 Processing helix chain 'H' and resid 12 through 37 removed outlier: 4.371A pdb=" N ARG H 37 " --> pdb=" O THR H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 69 No H-bonds generated for 'chain 'H' and resid 67 through 69' Processing helix chain 'H' and resid 104 through 107 No H-bonds generated for 'chain 'H' and resid 104 through 107' Processing helix chain 'H' and resid 110 through 112 No H-bonds generated for 'chain 'H' and resid 110 through 112' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 211 through 215 Processing helix chain 'H' and resid 227 through 243 removed outlier: 4.169A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 13 through 37 Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'B' and resid 14 through 45 Processing helix chain 'D' and resid 4 through 10 Processing helix chain 'D' and resid 13 through 37 Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'E' and resid 14 through 45 Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 13 through 37 Processing helix chain 'F' and resid 43 through 50 Processing helix chain 'G' 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 removed outlier: 3.503A pdb=" N ALA I 48 " --> pdb=" O LEU I 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 45 Processing helix chain 'K' and resid 4 through 9 Processing helix chain 'K' and resid 13 through 37 Processing helix chain 'K' and resid 43 through 50 Processing helix chain 'N' and resid 14 through 45 Processing helix chain 'O' and resid 4 through 9 Processing helix chain 'O' and resid 13 through 37 Processing helix chain 'O' and resid 43 through 50 Processing helix chain 'P' and resid 14 through 45 Processing helix chain 'Q' and resid 4 through 9 Processing helix chain 'Q' and resid 13 through 37 Processing helix chain 'Q' and resid 43 through 51 Processing helix chain 'R' and resid 14 through 45 Processing helix chain 'S' and resid 4 through 9 Processing helix chain 'S' and resid 13 through 37 Processing helix chain 'S' and resid 43 through 50 Processing helix chain 'T' and resid 14 through 45 Processing helix chain 'U' and resid 4 through 10 Processing helix chain 'U' and resid 13 through 37 Processing helix chain 'U' and resid 43 through 51 Processing helix chain 'V' and resid 14 through 45 removed outlier: 3.626A pdb=" N GLU V 19 " --> pdb=" O GLU V 15 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 9 removed outlier: 3.516A pdb=" N TRP W 8 " --> pdb=" O TYR W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 37 Processing helix chain 'W' and resid 43 through 51 Processing helix chain 'C' and resid 14 through 45 Processing helix chain '3' and resid 5 through 10 Processing helix chain '3' and resid 13 through 37 Processing helix chain '3' and resid 43 through 50 Processing helix chain 'Z' and resid 14 through 45 Processing helix chain '1' and resid 5 through 10 Processing helix chain '1' and resid 13 through 37 Processing helix chain '1' and resid 43 through 51 Processing helix chain '2' and resid 14 through 45 Processing helix chain '7' and resid 4 through 9 Processing helix chain '7' and resid 13 through 37 Processing helix chain '8' and resid 14 through 45 Processing helix chain '9' and resid 4 through 9 Processing helix chain '9' and resid 13 through 37 Processing helix chain '9' and resid 43 through 50 Processing helix chain '0' and resid 14 through 45 Processing helix chain 'X' and resid 17 through 54 Processing helix chain 'Y' and resid 6 through 28 Processing helix chain 'Y' and resid 32 through 47 Processing sheet with id= A, first strand: chain 'L' and resid 24 through 26 removed outlier: 4.179A pdb=" N PHE L 24 " --> pdb=" O VAL L 31 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 62 through 66 removed outlier: 4.357A pdb=" N GLY H 71 " --> pdb=" O LEU H 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 87 through 89 Processing sheet with id= D, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.922A pdb=" N GLU H 180 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE H 167 " --> pdb=" O PHE H 178 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE H 178 " --> pdb=" O ILE H 167 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 202 through 204 removed outlier: 3.787A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) 1147 hydrogen bonds defined for protein. 3300 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: 5.95 Time building geometry restraints manager: 9.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.34: 5603 1.34 - 1.55: 16521 1.55 - 1.76: 901 1.76 - 1.96: 175 1.96 - 2.17: 128 Bond restraints: 23328 Sorted by residual: bond pdb=" C3C BPB L 303 " pdb=" CAC BPB L 303 " ideal model delta sigma weight residual 1.334 1.557 -0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C3C BPB M 403 " pdb=" CAC BPB M 403 " ideal model delta sigma weight residual 1.334 1.547 -0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C16 SPO T 102 " pdb=" C17 SPO T 102 " ideal model delta sigma weight residual 1.444 1.650 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C23 SPO E 102 " pdb=" C25 SPO E 102 " ideal model delta sigma weight residual 1.448 1.652 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C16 SPO 3 104 " pdb=" C17 SPO 3 104 " ideal model delta sigma weight residual 1.444 1.647 -0.203 2.00e-02 2.50e+03 1.03e+02 ... (remaining 23323 not shown) Histogram of bond angle deviations from ideal: 31.78 - 59.97: 1 59.97 - 88.17: 118 88.17 - 116.36: 15468 116.36 - 144.55: 16218 144.55 - 172.75: 201 Bond angle restraints: 32006 Sorted by residual: angle pdb=" C29 SPO V 101 " pdb=" C28 SPO V 101 " pdb=" C30 SPO V 101 " ideal model delta sigma weight residual 115.38 31.78 83.60 3.00e+00 1.11e-01 7.77e+02 angle pdb=" C34 SPO J 103 " pdb=" C33 SPO J 103 " pdb=" C35 SPO J 103 " ideal model delta sigma weight residual 115.46 60.59 54.87 3.00e+00 1.11e-01 3.34e+02 angle pdb=" C34 SPO 3 104 " pdb=" C33 SPO 3 104 " pdb=" C35 SPO 3 104 " ideal model delta sigma weight residual 115.46 61.87 53.59 3.00e+00 1.11e-01 3.19e+02 angle pdb=" C32 SPO U 104 " pdb=" C33 SPO U 104 " pdb=" C35 SPO U 104 " ideal model delta sigma weight residual 120.11 172.75 -52.64 3.00e+00 1.11e-01 3.08e+02 angle pdb=" C32 SPO M 405 " pdb=" C33 SPO M 405 " pdb=" C35 SPO M 405 " ideal model delta sigma weight residual 120.11 172.09 -51.98 3.00e+00 1.11e-01 3.00e+02 ... (remaining 32001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 11898 35.92 - 71.85: 548 71.85 - 107.77: 64 107.77 - 143.69: 6 143.69 - 179.61: 2 Dihedral angle restraints: 12518 sinusoidal: 5917 harmonic: 6601 Sorted by residual: dihedral pdb=" C1 BCL L 307 " pdb=" C2 BCL L 307 " pdb=" C3 BCL L 307 " pdb=" C5 BCL L 307 " ideal model delta sinusoidal sigma weight residual 180.00 0.39 179.61 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C6 U10 L 305 " pdb=" C7 U10 L 305 " pdb=" C8 U10 L 305 " pdb=" C9 U10 L 305 " ideal model delta sinusoidal sigma weight residual 101.51 -128.74 -129.75 1 2.00e+01 2.50e-03 3.93e+01 dihedral pdb=" C3M U10 M 404 " pdb=" C3 U10 M 404 " pdb=" O3 U10 M 404 " pdb=" C4 U10 M 404 " ideal model delta sinusoidal sigma weight residual 244.38 125.42 118.96 1 2.00e+01 2.50e-03 3.56e+01 ... (remaining 12515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2339 0.048 - 0.095: 660 0.095 - 0.143: 95 0.143 - 0.191: 8 0.191 - 0.238: 3 Chirality restraints: 3105 Sorted by residual: chirality pdb=" CA PRO H 78 " pdb=" N PRO H 78 " pdb=" C PRO H 78 " pdb=" CB PRO H 78 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C2C BPB M 403 " pdb=" C1C BPB M 403 " pdb=" C3C BPB M 403 " pdb=" CMC BPB M 403 " both_signs ideal model delta sigma weight residual False -2.78 -2.56 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA PHE L 216 " pdb=" N PHE L 216 " pdb=" C PHE L 216 " pdb=" CB PHE L 216 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.87e-01 ... (remaining 3102 not shown) Planarity restraints: 3909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2C BPB L 303 " -0.329 2.00e-02 2.50e+03 5.00e-01 3.13e+03 pdb=" C3C BPB L 303 " 0.497 2.00e-02 2.50e+03 pdb=" C4C BPB L 303 " -0.262 2.00e-02 2.50e+03 pdb=" CAC BPB L 303 " 0.688 2.00e-02 2.50e+03 pdb=" CBC BPB L 303 " -0.595 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2C BPB M 403 " 0.022 2.00e-02 2.50e+03 2.50e-01 7.83e+02 pdb=" C3C BPB M 403 " 0.326 2.00e-02 2.50e+03 pdb=" C4C BPB M 403 " -0.134 2.00e-02 2.50e+03 pdb=" CAC BPB M 403 " -0.395 2.00e-02 2.50e+03 pdb=" CBC BPB M 403 " 0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY H 77 " 0.109 5.00e-02 4.00e+02 1.50e-01 3.61e+01 pdb=" N PRO H 78 " -0.259 5.00e-02 4.00e+02 pdb=" CA PRO H 78 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO H 78 " 0.077 5.00e-02 4.00e+02 ... (remaining 3906 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 317 2.61 - 3.19: 17634 3.19 - 3.76: 35695 3.76 - 4.33: 53326 4.33 - 4.90: 85753 Nonbonded interactions: 192725 Sorted by model distance: nonbonded pdb=" OG1 THR O 38 " pdb=" O SER O 40 " model vdw 2.042 2.440 nonbonded pdb=" OG1 THR W 38 " pdb=" O SER W 40 " model vdw 2.116 2.440 nonbonded pdb=" OG SER H 80 " pdb=" OD1 ASP H 82 " model vdw 2.124 2.440 nonbonded pdb=" NZ LYS S 6 " pdb=" OE1 GLU V 19 " model vdw 2.132 2.520 nonbonded pdb=" O SER 3 40 " pdb=" NH1 ARG Z 46 " model vdw 2.152 2.520 ... (remaining 192720 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 '0' and resid 8 through 49) selection = (chain '8' and resid 8 through 49) selection = (chain 'B' and resid 8 through 49) selection = (chain 'C' and resid 8 through 49) selection = (chain 'E' and resid 8 through 49) selection = (chain 'G' and resid 8 through 49) selection = (chain 'J' and resid 8 through 49) selection = (chain 'N' and resid 8 through 49) selection = (chain 'P' and resid 8 through 49) selection = (chain 'R' and resid 8 through 49) selection = (chain 'T' and resid 8 through 49) selection = (chain 'V' and resid 8 through 49) selection = chain 'Z' } ncs_group { reference = (chain '1' and resid 2 through 54) selection = (chain '3' and resid 2 through 54) selection = (chain '9' and resid 2 through 54) selection = (chain 'A' and resid 2 through 54) selection = (chain 'D' and resid 2 through 54) selection = (chain 'F' and resid 2 through 54) selection = (chain 'I' and resid 2 through 54) selection = (chain 'K' and resid 2 through 54) selection = (chain 'O' and resid 2 through 54) selection = (chain 'Q' and resid 2 through 54) selection = (chain 'S' and resid 2 through 54) selection = (chain 'U' and resid 2 through 54) selection = (chain 'W' and resid 2 through 54) } 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: 0.780 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: 4.840 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 56.770 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 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 0.223 23328 Z= 0.968 Angle : 3.948 83.604 32006 Z= 1.342 Chirality : 0.043 0.238 3105 Planarity : 0.012 0.500 3909 Dihedral : 19.174 179.613 8276 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.68 % Allowed : 8.52 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.17), residues: 2217 helix: 1.88 (0.12), residues: 1503 sheet: -0.85 (0.75), residues: 44 loop : -0.53 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.002 TRP L 272 HIS 0.014 0.002 HIS L 230 PHE 0.090 0.002 PHE M 216 TYR 0.026 0.002 TYR M 198 ARG 0.012 0.001 ARG M 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 304 time to evaluate : 2.164 Fit side-chains REVERT: M 168 MET cc_start: 0.8516 (mmm) cc_final: 0.7794 (mmm) REVERT: M 261 THR cc_start: 0.8395 (m) cc_final: 0.8081 (p) REVERT: H 130 LYS cc_start: 0.7905 (tttt) cc_final: 0.7657 (tttm) REVERT: B 19 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6059 (tm-30) REVERT: B 40 LEU cc_start: 0.8107 (mt) cc_final: 0.7760 (tt) REVERT: D 1 MET cc_start: 0.5152 (mtp) cc_final: 0.4936 (mtp) REVERT: F 3 LYS cc_start: 0.7589 (mttp) cc_final: 0.7299 (mtmm) REVERT: I 10 ILE cc_start: 0.7574 (pt) cc_final: 0.7325 (pp) REVERT: J 24 TYR cc_start: 0.8297 (t80) cc_final: 0.8040 (t80) REVERT: O 5 TYR cc_start: 0.7297 (p90) cc_final: 0.6871 (p90) REVERT: U 9 MET cc_start: 0.7312 (mtm) cc_final: 0.6723 (mtm) REVERT: U 15 ARG cc_start: 0.7075 (mtp180) cc_final: 0.6767 (mtp85) REVERT: U 46 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7472 (pp) REVERT: U 51 TYR cc_start: 0.8052 (m-80) cc_final: 0.7832 (m-80) REVERT: W 6 LYS cc_start: 0.6967 (mttm) cc_final: 0.6349 (ttmm) REVERT: W 15 ARG cc_start: 0.6321 (mmm-85) cc_final: 0.5703 (mmt180) REVERT: Z 25 MET cc_start: 0.7913 (mmp) cc_final: 0.7652 (mmm) REVERT: 8 22 SER cc_start: 0.7615 (t) cc_final: 0.7241 (m) REVERT: 8 25 MET cc_start: 0.8123 (mmp) cc_final: 0.7811 (mmm) REVERT: Y 6 GLU cc_start: 0.5518 (tp30) cc_final: 0.5213 (tm-30) outliers start: 13 outliers final: 5 residues processed: 311 average time/residue: 1.3549 time to fit residues: 480.5732 Evaluate side-chains 282 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 275 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain 3 residue 39 PRO Chi-restraints excluded: chain 0 residue 22 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 4 GLN K 20 GLN O 20 GLN C 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 23328 Z= 0.288 Angle : 1.124 42.275 32006 Z= 0.416 Chirality : 0.041 0.141 3105 Planarity : 0.005 0.075 3909 Dihedral : 18.061 179.677 4281 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.42 % Allowed : 9.05 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.17), residues: 2217 helix: 2.00 (0.12), residues: 1502 sheet: -0.85 (0.77), residues: 44 loop : -0.43 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP L 272 HIS 0.013 0.002 HIS M 182 PHE 0.050 0.002 PHE M 216 TYR 0.019 0.002 TYR M 198 ARG 0.009 0.001 ARG M 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 295 time to evaluate : 2.013 Fit side-chains REVERT: L 258 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.6751 (mm-40) REVERT: L 271 TRP cc_start: 0.8077 (p90) cc_final: 0.7872 (p90) REVERT: M 93 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8317 (t) REVERT: M 168 MET cc_start: 0.8483 (mmm) cc_final: 0.7948 (mmm) REVERT: M 261 THR cc_start: 0.8450 (m) cc_final: 0.8166 (p) REVERT: H 1 MET cc_start: 0.6645 (tpp) cc_final: 0.6423 (tpp) REVERT: H 130 LYS cc_start: 0.7894 (tttt) cc_final: 0.7662 (tttm) REVERT: H 177 ARG cc_start: 0.7293 (mtt-85) cc_final: 0.6276 (mtp180) REVERT: B 19 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6113 (tm-30) REVERT: B 40 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7715 (tp) REVERT: D 9 MET cc_start: 0.7264 (mtm) cc_final: 0.7041 (mtm) REVERT: I 5 TYR cc_start: 0.7301 (p90) cc_final: 0.6913 (p90) REVERT: I 10 ILE cc_start: 0.7705 (pt) cc_final: 0.7438 (pp) REVERT: J 23 VAL cc_start: 0.7589 (OUTLIER) cc_final: 0.7356 (t) REVERT: O 10 ILE cc_start: 0.7519 (mt) cc_final: 0.7162 (mm) REVERT: O 20 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7139 (tt0) REVERT: P 40 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7368 (mm) REVERT: T 25 MET cc_start: 0.8293 (mmm) cc_final: 0.8021 (mmp) REVERT: U 9 MET cc_start: 0.7344 (mtm) cc_final: 0.6805 (mtm) REVERT: U 15 ARG cc_start: 0.7000 (mtp180) cc_final: 0.6658 (mtp85) REVERT: W 15 ARG cc_start: 0.6330 (mmm-85) cc_final: 0.5968 (mmt180) REVERT: Z 25 MET cc_start: 0.7883 (mmp) cc_final: 0.7607 (mmm) REVERT: 8 22 SER cc_start: 0.7610 (t) cc_final: 0.7261 (m) REVERT: X 27 MET cc_start: 0.6280 (mtt) cc_final: 0.5967 (mtt) REVERT: Y 6 GLU cc_start: 0.5495 (tp30) cc_final: 0.5225 (tm-30) outliers start: 46 outliers final: 24 residues processed: 318 average time/residue: 1.2865 time to fit residues: 468.0059 Evaluate side-chains 306 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 275 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 258 GLN Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 3 LYS Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain 3 residue 9 MET Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain Z residue 20 LEU Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 8 residue 36 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 196 optimal weight: 20.0000 chunk 212 optimal weight: 0.9990 chunk 175 optimal weight: 10.0000 chunk 194 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN C 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 23328 Z= 0.297 Angle : 1.073 42.960 32006 Z= 0.401 Chirality : 0.041 0.149 3105 Planarity : 0.005 0.068 3909 Dihedral : 17.647 179.648 4271 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.37 % Allowed : 9.89 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.17), residues: 2217 helix: 2.01 (0.12), residues: 1497 sheet: -0.97 (0.86), residues: 36 loop : -0.43 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 272 HIS 0.012 0.002 HIS M 182 PHE 0.030 0.002 PHE M 216 TYR 0.017 0.002 TYR D 51 ARG 0.008 0.001 ARG M 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 288 time to evaluate : 2.214 Fit side-chains REVERT: L 47 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7610 (mt) REVERT: L 216 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7520 (m-80) REVERT: L 258 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.6767 (mm-40) REVERT: M 93 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8374 (t) REVERT: M 168 MET cc_start: 0.8483 (mmm) cc_final: 0.7955 (mmm) REVERT: M 233 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.6078 (mtm-85) REVERT: M 235 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7149 (mp) REVERT: M 261 THR cc_start: 0.8469 (m) cc_final: 0.8189 (p) REVERT: H 130 LYS cc_start: 0.7943 (tttt) cc_final: 0.7544 (tttm) REVERT: H 170 ASP cc_start: 0.7832 (t70) cc_final: 0.7544 (t0) REVERT: H 177 ARG cc_start: 0.7102 (mtt-85) cc_final: 0.6307 (mtp180) REVERT: H 193 MET cc_start: 0.7798 (tpt) cc_final: 0.7590 (mmm) REVERT: B 19 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.5987 (tm-30) REVERT: B 40 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7690 (tp) REVERT: D 9 MET cc_start: 0.7252 (mtm) cc_final: 0.6938 (mtm) REVERT: F 3 LYS cc_start: 0.7537 (mttp) cc_final: 0.7300 (mttm) REVERT: I 5 TYR cc_start: 0.7409 (p90) cc_final: 0.6891 (p90) REVERT: I 10 ILE cc_start: 0.7773 (pt) cc_final: 0.7516 (pp) REVERT: I 15 ARG cc_start: 0.5847 (mtm110) cc_final: 0.5198 (mmt90) REVERT: O 5 TYR cc_start: 0.7041 (p90) cc_final: 0.6695 (p90) REVERT: O 10 ILE cc_start: 0.7529 (mt) cc_final: 0.7208 (mm) REVERT: P 40 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7454 (mm) REVERT: Q 12 ASP cc_start: 0.7972 (t0) cc_final: 0.7584 (t0) REVERT: R 18 GLN cc_start: 0.7149 (mt0) cc_final: 0.6129 (mt0) REVERT: S 15 ARG cc_start: 0.6555 (mtp85) cc_final: 0.5712 (mtp-110) REVERT: U 9 MET cc_start: 0.7322 (mtm) cc_final: 0.6730 (mtm) REVERT: U 46 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7414 (pp) REVERT: W 6 LYS cc_start: 0.7048 (mttm) cc_final: 0.6360 (ttmm) REVERT: W 9 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.7064 (mtp) REVERT: W 15 ARG cc_start: 0.6363 (mmm-85) cc_final: 0.6064 (mtt180) REVERT: Z 25 MET cc_start: 0.8017 (mmp) cc_final: 0.7709 (mmm) REVERT: 8 22 SER cc_start: 0.7689 (t) cc_final: 0.7351 (m) REVERT: 9 30 MET cc_start: 0.7172 (ttm) cc_final: 0.6690 (ttm) REVERT: X 27 MET cc_start: 0.6428 (mtt) cc_final: 0.6130 (mtt) REVERT: Y 6 GLU cc_start: 0.5491 (tp30) cc_final: 0.5241 (tm-30) outliers start: 64 outliers final: 33 residues processed: 322 average time/residue: 1.3701 time to fit residues: 503.7319 Evaluate side-chains 322 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 278 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 258 GLN Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 233 ARG Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 3 LYS Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 9 MET Chi-restraints excluded: chain 3 residue 9 MET Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain 3 residue 47 SER Chi-restraints excluded: chain Z residue 20 LEU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 8 residue 36 ILE Chi-restraints excluded: chain X residue 21 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN T 16 GLN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 23328 Z= 0.371 Angle : 1.134 42.701 32006 Z= 0.428 Chirality : 0.044 0.165 3105 Planarity : 0.006 0.080 3909 Dihedral : 17.856 179.578 4271 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.84 % Allowed : 11.26 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.17), residues: 2217 helix: 1.79 (0.12), residues: 1495 sheet: -1.08 (0.85), residues: 36 loop : -0.59 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 157 HIS 0.011 0.002 HIS L 168 PHE 0.031 0.002 PHE M 216 TYR 0.020 0.002 TYR D 51 ARG 0.010 0.001 ARG M 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 279 time to evaluate : 2.454 Fit side-chains REVERT: L 62 GLN cc_start: 0.7800 (mt0) cc_final: 0.7395 (mt0) REVERT: L 216 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.7516 (m-80) REVERT: L 258 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.6873 (mm-40) REVERT: M 62 SER cc_start: 0.8713 (m) cc_final: 0.8080 (p) REVERT: M 93 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8463 (t) REVERT: M 233 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.6061 (mtm-85) REVERT: M 235 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7229 (mp) REVERT: M 261 THR cc_start: 0.8516 (m) cc_final: 0.8217 (p) REVERT: H 106 LYS cc_start: 0.7193 (mmtt) cc_final: 0.6631 (tttp) REVERT: H 130 LYS cc_start: 0.7937 (tttt) cc_final: 0.7536 (tttm) REVERT: H 170 ASP cc_start: 0.7826 (t70) cc_final: 0.7498 (t0) REVERT: H 177 ARG cc_start: 0.7156 (mtt-85) cc_final: 0.6285 (mtp180) REVERT: H 193 MET cc_start: 0.7843 (tpt) cc_final: 0.7615 (mmm) REVERT: B 19 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6032 (tm-30) REVERT: F 9 MET cc_start: 0.7504 (mtp) cc_final: 0.6889 (mpp) REVERT: I 5 TYR cc_start: 0.7466 (p90) cc_final: 0.6870 (p90) REVERT: I 6 LYS cc_start: 0.8319 (mttt) cc_final: 0.8071 (mptp) REVERT: I 10 ILE cc_start: 0.7828 (pt) cc_final: 0.7544 (pp) REVERT: I 12 ASP cc_start: 0.7514 (t70) cc_final: 0.7261 (t70) REVERT: O 1 MET cc_start: 0.5673 (mmt) cc_final: 0.5395 (tpt) REVERT: O 10 ILE cc_start: 0.7522 (mt) cc_final: 0.7206 (mm) REVERT: Q 12 ASP cc_start: 0.8098 (t0) cc_final: 0.7739 (t0) REVERT: R 18 GLN cc_start: 0.7173 (mt0) cc_final: 0.6171 (mt0) REVERT: S 3 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.6867 (mmtt) REVERT: S 15 ARG cc_start: 0.6741 (mtp85) cc_final: 0.5936 (mtp-110) REVERT: U 46 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7457 (pp) REVERT: W 6 LYS cc_start: 0.6900 (mttm) cc_final: 0.6298 (ttmm) REVERT: W 9 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7034 (mtp) REVERT: W 15 ARG cc_start: 0.6415 (mmm-85) cc_final: 0.6102 (mtt180) REVERT: 8 22 SER cc_start: 0.7551 (t) cc_final: 0.7252 (m) REVERT: 9 30 MET cc_start: 0.7137 (ttm) cc_final: 0.6721 (ttm) REVERT: 0 9 TYR cc_start: 0.8139 (m-10) cc_final: 0.7933 (m-10) REVERT: 0 18 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.7120 (mt0) REVERT: X 27 MET cc_start: 0.6727 (mtt) cc_final: 0.5375 (mtt) REVERT: Y 6 GLU cc_start: 0.5398 (tp30) cc_final: 0.5147 (tm-30) REVERT: Y 12 MET cc_start: 0.6208 (mtp) cc_final: 0.5970 (mtt) outliers start: 73 outliers final: 40 residues processed: 319 average time/residue: 1.3224 time to fit residues: 481.5255 Evaluate side-chains 321 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 271 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 258 GLN Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 233 ARG Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 47 SER Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 3 LYS Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 9 MET Chi-restraints excluded: chain W residue 54 VAL Chi-restraints excluded: chain 3 residue 9 MET Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain 3 residue 47 SER Chi-restraints excluded: chain Z residue 20 LEU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 8 residue 6 ASP Chi-restraints excluded: chain 8 residue 36 ILE Chi-restraints excluded: chain 0 residue 18 GLN Chi-restraints excluded: chain X residue 21 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 11 GLN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN U 20 GLN C 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 23328 Z= 0.265 Angle : 1.034 42.629 32006 Z= 0.387 Chirality : 0.040 0.148 3105 Planarity : 0.005 0.066 3909 Dihedral : 17.377 179.615 4271 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.26 % Allowed : 12.15 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.17), residues: 2217 helix: 2.08 (0.12), residues: 1494 sheet: -1.06 (0.86), residues: 36 loop : -0.52 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 157 HIS 0.012 0.002 HIS M 182 PHE 0.028 0.002 PHE M 216 TYR 0.014 0.002 TYR M 198 ARG 0.006 0.001 ARG O 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 284 time to evaluate : 2.394 Fit side-chains REVERT: L 47 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7613 (mt) REVERT: L 62 GLN cc_start: 0.7795 (mt0) cc_final: 0.7473 (mt0) REVERT: L 216 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.7525 (m-80) REVERT: L 258 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.6691 (mm-40) REVERT: M 93 SER cc_start: 0.8640 (OUTLIER) cc_final: 0.8406 (t) REVERT: M 233 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.6058 (mtm-85) REVERT: M 235 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7102 (mp) REVERT: M 261 THR cc_start: 0.8450 (m) cc_final: 0.8190 (p) REVERT: H 106 LYS cc_start: 0.7241 (mmtt) cc_final: 0.6677 (tttp) REVERT: H 130 LYS cc_start: 0.7868 (tttt) cc_final: 0.7470 (tttm) REVERT: H 170 ASP cc_start: 0.7812 (t70) cc_final: 0.7537 (t0) REVERT: H 177 ARG cc_start: 0.7149 (mtt-85) cc_final: 0.6352 (mtp180) REVERT: B 19 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.5927 (tm-30) REVERT: B 40 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7688 (tp) REVERT: I 5 TYR cc_start: 0.7462 (p90) cc_final: 0.6760 (p90) REVERT: I 10 ILE cc_start: 0.7717 (pt) cc_final: 0.7496 (pp) REVERT: I 12 ASP cc_start: 0.7553 (t70) cc_final: 0.7293 (t70) REVERT: I 15 ARG cc_start: 0.5882 (mtm110) cc_final: 0.4769 (mmm160) REVERT: O 1 MET cc_start: 0.5425 (mmt) cc_final: 0.5124 (tpt) REVERT: O 5 TYR cc_start: 0.7044 (p90) cc_final: 0.6687 (p90) REVERT: O 9 MET cc_start: 0.7597 (mtp) cc_final: 0.7305 (mtp) REVERT: O 10 ILE cc_start: 0.7508 (mt) cc_final: 0.7195 (mm) REVERT: O 20 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7111 (tt0) REVERT: P 40 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7425 (mm) REVERT: Q 12 ASP cc_start: 0.7933 (t0) cc_final: 0.7522 (t0) REVERT: R 18 GLN cc_start: 0.7233 (mt0) cc_final: 0.6211 (mt0) REVERT: U 9 MET cc_start: 0.7183 (mtm) cc_final: 0.6598 (mtm) REVERT: U 46 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7397 (pp) REVERT: W 5 TYR cc_start: 0.7494 (p90) cc_final: 0.7157 (p90) REVERT: W 9 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.7085 (mtp) REVERT: 3 1 MET cc_start: 0.2272 (mtm) cc_final: 0.1768 (mtt) REVERT: Z 25 MET cc_start: 0.7904 (mmp) cc_final: 0.7680 (mmm) REVERT: 8 22 SER cc_start: 0.7689 (t) cc_final: 0.7353 (m) REVERT: 8 36 ILE cc_start: 0.7603 (mt) cc_final: 0.7195 (mt) REVERT: 9 30 MET cc_start: 0.7102 (ttm) cc_final: 0.6676 (ttm) REVERT: X 27 MET cc_start: 0.6684 (mtt) cc_final: 0.5386 (mtt) REVERT: Y 6 GLU cc_start: 0.5379 (tp30) cc_final: 0.5095 (tm-30) outliers start: 62 outliers final: 35 residues processed: 320 average time/residue: 1.3228 time to fit residues: 484.5589 Evaluate side-chains 318 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 271 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 258 GLN Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 233 ARG Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 3 LYS Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 9 MET Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain W residue 54 VAL Chi-restraints excluded: chain 3 residue 9 MET Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain 3 residue 47 SER Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain X residue 42 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 208 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 109 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 GLN C 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23328 Z= 0.147 Angle : 0.924 42.226 32006 Z= 0.341 Chirality : 0.035 0.136 3105 Planarity : 0.004 0.052 3909 Dihedral : 16.593 179.516 4271 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.16 % Allowed : 13.57 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.49 (0.18), residues: 2217 helix: 2.58 (0.12), residues: 1513 sheet: -0.73 (0.88), residues: 36 loop : -0.44 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 157 HIS 0.007 0.001 HIS M 182 PHE 0.015 0.001 PHE M 216 TYR 0.012 0.001 TYR O 41 ARG 0.004 0.000 ARG O 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 296 time to evaluate : 2.244 Fit side-chains REVERT: L 47 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7559 (mt) REVERT: L 62 GLN cc_start: 0.7765 (mt0) cc_final: 0.7380 (mt0) REVERT: L 216 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7560 (m-80) REVERT: L 235 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7830 (mt) REVERT: M 93 SER cc_start: 0.8620 (p) cc_final: 0.8413 (t) REVERT: M 168 MET cc_start: 0.8408 (mmm) cc_final: 0.7864 (mmm) REVERT: M 261 THR cc_start: 0.8272 (m) cc_final: 0.7974 (p) REVERT: H 60 LYS cc_start: 0.6592 (mptp) cc_final: 0.6249 (mttt) REVERT: H 106 LYS cc_start: 0.7304 (mmtt) cc_final: 0.6745 (tttp) REVERT: H 130 LYS cc_start: 0.7844 (tttt) cc_final: 0.7458 (tttm) REVERT: H 177 ARG cc_start: 0.7095 (mtt-85) cc_final: 0.6355 (mtp180) REVERT: A 30 MET cc_start: 0.7514 (ttt) cc_final: 0.7128 (ttp) REVERT: I 5 TYR cc_start: 0.7488 (p90) cc_final: 0.6750 (p90) REVERT: I 10 ILE cc_start: 0.7651 (pt) cc_final: 0.7400 (pp) REVERT: I 11 PHE cc_start: 0.8070 (m-80) cc_final: 0.7651 (m-10) REVERT: I 12 ASP cc_start: 0.7522 (t70) cc_final: 0.7299 (t70) REVERT: I 15 ARG cc_start: 0.5726 (mtm110) cc_final: 0.4782 (mtt-85) REVERT: N 20 LEU cc_start: 0.7610 (tt) cc_final: 0.7407 (tt) REVERT: O 1 MET cc_start: 0.5360 (mmt) cc_final: 0.5049 (tpt) REVERT: O 5 TYR cc_start: 0.7084 (p90) cc_final: 0.6698 (p90) REVERT: O 9 MET cc_start: 0.7527 (mtp) cc_final: 0.7286 (mtp) REVERT: O 10 ILE cc_start: 0.7521 (mt) cc_final: 0.7181 (mm) REVERT: O 20 GLN cc_start: 0.7894 (tt0) cc_final: 0.7607 (tt0) REVERT: Q 12 ASP cc_start: 0.8003 (t0) cc_final: 0.7612 (t0) REVERT: R 18 GLN cc_start: 0.7170 (mt0) cc_final: 0.6279 (mt0) REVERT: R 25 MET cc_start: 0.8104 (mmm) cc_final: 0.7863 (mmm) REVERT: U 9 MET cc_start: 0.7246 (mtm) cc_final: 0.6652 (mtm) REVERT: W 5 TYR cc_start: 0.7419 (p90) cc_final: 0.7115 (p90) REVERT: W 37 SER cc_start: 0.7792 (m) cc_final: 0.7302 (p) REVERT: 3 1 MET cc_start: 0.2005 (mtm) cc_final: 0.1542 (mtt) REVERT: 3 30 MET cc_start: 0.7641 (ttp) cc_final: 0.7409 (ttm) REVERT: 2 36 ILE cc_start: 0.6179 (OUTLIER) cc_final: 0.5948 (mm) REVERT: 8 22 SER cc_start: 0.7633 (t) cc_final: 0.7231 (m) REVERT: 8 25 MET cc_start: 0.7996 (mmp) cc_final: 0.7711 (mmm) REVERT: 8 36 ILE cc_start: 0.7674 (mt) cc_final: 0.7291 (mt) REVERT: 8 43 TYR cc_start: 0.7575 (t80) cc_final: 0.7274 (t80) REVERT: 9 1 MET cc_start: 0.5504 (ttt) cc_final: 0.5290 (ttm) REVERT: 9 30 MET cc_start: 0.7058 (ttm) cc_final: 0.6644 (ttm) REVERT: 0 19 GLU cc_start: 0.6239 (tp30) cc_final: 0.5799 (mm-30) REVERT: X 27 MET cc_start: 0.6277 (mtt) cc_final: 0.5991 (mtt) REVERT: Y 6 GLU cc_start: 0.5273 (tp30) cc_final: 0.4993 (tm-30) outliers start: 41 outliers final: 21 residues processed: 319 average time/residue: 1.2340 time to fit residues: 454.6844 Evaluate side-chains 304 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 279 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 3 LYS Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain 3 residue 47 SER Chi-restraints excluded: chain 2 residue 36 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23328 Z= 0.235 Angle : 0.991 42.494 32006 Z= 0.371 Chirality : 0.039 0.149 3105 Planarity : 0.004 0.064 3909 Dihedral : 16.768 179.611 4268 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.89 % Allowed : 13.36 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.35 (0.17), residues: 2217 helix: 2.46 (0.12), residues: 1495 sheet: -0.93 (0.86), residues: 36 loop : -0.34 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 157 HIS 0.011 0.002 HIS M 182 PHE 0.017 0.002 PHE H 20 TYR 0.015 0.001 TYR M 198 ARG 0.006 0.001 ARG O 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 281 time to evaluate : 2.120 Fit side-chains REVERT: L 62 GLN cc_start: 0.7806 (mt0) cc_final: 0.7527 (mt0) REVERT: L 216 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7556 (m-80) REVERT: M 93 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.8384 (t) REVERT: M 168 MET cc_start: 0.8458 (mmm) cc_final: 0.7819 (mmm) REVERT: M 235 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7364 (mp) REVERT: M 261 THR cc_start: 0.8401 (m) cc_final: 0.8147 (p) REVERT: M 278 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6970 (tp) REVERT: H 106 LYS cc_start: 0.7316 (mmtt) cc_final: 0.6736 (tttp) REVERT: H 130 LYS cc_start: 0.7751 (tttt) cc_final: 0.7417 (tttm) REVERT: H 177 ARG cc_start: 0.7127 (mtt-85) cc_final: 0.6306 (mtp180) REVERT: A 30 MET cc_start: 0.7529 (ttt) cc_final: 0.7090 (ttp) REVERT: B 40 LEU cc_start: 0.8075 (tp) cc_final: 0.7851 (tp) REVERT: G 19 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6695 (tt0) REVERT: I 5 TYR cc_start: 0.7467 (p90) cc_final: 0.6799 (p90) REVERT: I 10 ILE cc_start: 0.7775 (pt) cc_final: 0.7485 (pp) REVERT: I 11 PHE cc_start: 0.8085 (m-80) cc_final: 0.7666 (m-10) REVERT: I 12 ASP cc_start: 0.7572 (t70) cc_final: 0.7309 (t70) REVERT: I 15 ARG cc_start: 0.5793 (mtm110) cc_final: 0.5053 (mtt-85) REVERT: O 1 MET cc_start: 0.5384 (mmt) cc_final: 0.5163 (tpt) REVERT: O 5 TYR cc_start: 0.7095 (p90) cc_final: 0.6715 (p90) REVERT: O 9 MET cc_start: 0.7531 (mtp) cc_final: 0.7295 (mtp) REVERT: O 10 ILE cc_start: 0.7507 (mt) cc_final: 0.7152 (mm) REVERT: O 20 GLN cc_start: 0.7548 (tt0) cc_final: 0.7279 (tt0) REVERT: Q 9 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7313 (mtm) REVERT: Q 12 ASP cc_start: 0.7989 (t0) cc_final: 0.7596 (t0) REVERT: R 18 GLN cc_start: 0.7235 (mt0) cc_final: 0.6261 (mt0) REVERT: U 9 MET cc_start: 0.7234 (mtm) cc_final: 0.6623 (mtm) REVERT: W 30 MET cc_start: 0.7758 (ttp) cc_final: 0.7501 (ttt) REVERT: 3 1 MET cc_start: 0.2084 (mtm) cc_final: 0.1616 (mtt) REVERT: 2 36 ILE cc_start: 0.6191 (OUTLIER) cc_final: 0.5959 (mm) REVERT: 8 22 SER cc_start: 0.7702 (t) cc_final: 0.7364 (m) REVERT: 8 36 ILE cc_start: 0.7635 (mt) cc_final: 0.7245 (mt) REVERT: 9 30 MET cc_start: 0.7097 (ttm) cc_final: 0.6705 (ttm) REVERT: X 27 MET cc_start: 0.6373 (mtt) cc_final: 0.6083 (mtt) REVERT: Y 6 GLU cc_start: 0.5338 (tp30) cc_final: 0.5067 (tm-30) outliers start: 55 outliers final: 30 residues processed: 313 average time/residue: 1.3099 time to fit residues: 470.6679 Evaluate side-chains 309 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 272 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain Q residue 9 MET Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain 3 residue 9 MET Chi-restraints excluded: chain 3 residue 47 SER Chi-restraints excluded: chain Z residue 20 LEU Chi-restraints excluded: chain 2 residue 36 ILE Chi-restraints excluded: chain 2 residue 37 VAL Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain X residue 42 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 chunk 102 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 23328 Z= 0.377 Angle : 1.121 42.943 32006 Z= 0.425 Chirality : 0.044 0.166 3105 Planarity : 0.005 0.078 3909 Dihedral : 17.422 179.748 4268 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.26 % Allowed : 13.41 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.17), residues: 2217 helix: 1.94 (0.12), residues: 1495 sheet: -1.06 (0.84), residues: 36 loop : -0.53 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 157 HIS 0.012 0.002 HIS A 32 PHE 0.020 0.002 PHE H 20 TYR 0.019 0.002 TYR M 198 ARG 0.009 0.001 ARG M 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 285 time to evaluate : 1.977 Fit side-chains REVERT: L 6 GLU cc_start: 0.8629 (tt0) cc_final: 0.8402 (tt0) REVERT: L 62 GLN cc_start: 0.7879 (mt0) cc_final: 0.7522 (mt0) REVERT: L 216 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7492 (m-80) REVERT: L 258 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7020 (mm-40) REVERT: M 62 SER cc_start: 0.8718 (m) cc_final: 0.8104 (p) REVERT: M 93 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8404 (t) REVERT: M 168 MET cc_start: 0.8543 (mmm) cc_final: 0.8116 (mmm) REVERT: M 233 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.6015 (mtm-85) REVERT: M 235 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7438 (mp) REVERT: M 261 THR cc_start: 0.8570 (m) cc_final: 0.8262 (p) REVERT: H 106 LYS cc_start: 0.7191 (mmtt) cc_final: 0.6627 (tttp) REVERT: H 130 LYS cc_start: 0.7908 (tttt) cc_final: 0.7538 (tttm) REVERT: H 177 ARG cc_start: 0.7025 (mtt-85) cc_final: 0.6349 (mtp180) REVERT: F 9 MET cc_start: 0.7533 (mtp) cc_final: 0.6912 (mpp) REVERT: I 5 TYR cc_start: 0.7474 (p90) cc_final: 0.6791 (p90) REVERT: I 10 ILE cc_start: 0.7849 (pt) cc_final: 0.7594 (pp) REVERT: I 12 ASP cc_start: 0.7573 (t70) cc_final: 0.7278 (t70) REVERT: O 9 MET cc_start: 0.7577 (mtp) cc_final: 0.7355 (mtp) REVERT: O 10 ILE cc_start: 0.7480 (mt) cc_final: 0.7148 (mm) REVERT: O 20 GLN cc_start: 0.7644 (tt0) cc_final: 0.7292 (tt0) REVERT: Q 12 ASP cc_start: 0.7993 (t0) cc_final: 0.7598 (t0) REVERT: R 18 GLN cc_start: 0.7310 (mt0) cc_final: 0.6283 (mt0) REVERT: S 15 ARG cc_start: 0.6801 (mtp85) cc_final: 0.5911 (mtp-110) REVERT: U 30 MET cc_start: 0.7042 (tpp) cc_final: 0.6606 (tpp) REVERT: U 46 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7485 (pp) REVERT: W 30 MET cc_start: 0.7703 (ttp) cc_final: 0.7442 (ttt) REVERT: Z 25 MET cc_start: 0.7826 (mmm) cc_final: 0.7473 (mmp) REVERT: 8 22 SER cc_start: 0.7541 (t) cc_final: 0.7243 (m) REVERT: 9 30 MET cc_start: 0.7185 (ttm) cc_final: 0.6842 (ttm) REVERT: 0 18 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.7189 (mt0) REVERT: X 27 MET cc_start: 0.6699 (mtt) cc_final: 0.5370 (mtt) REVERT: Y 6 GLU cc_start: 0.5502 (tp30) cc_final: 0.5252 (tm-30) outliers start: 62 outliers final: 40 residues processed: 326 average time/residue: 1.3273 time to fit residues: 493.6205 Evaluate side-chains 320 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 273 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 258 GLN Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 233 ARG Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain 3 residue 9 MET Chi-restraints excluded: chain 3 residue 47 SER Chi-restraints excluded: chain Z residue 20 LEU Chi-restraints excluded: chain 2 residue 37 VAL Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 8 residue 14 ASP Chi-restraints excluded: chain 8 residue 36 ILE Chi-restraints excluded: chain 0 residue 18 GLN Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain Y residue 36 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 175 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 193 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23328 Z= 0.167 Angle : 0.944 42.453 32006 Z= 0.351 Chirality : 0.036 0.138 3105 Planarity : 0.004 0.050 3909 Dihedral : 16.377 179.450 4268 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.42 % Allowed : 14.47 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.47 (0.17), residues: 2217 helix: 2.56 (0.12), residues: 1494 sheet: -0.89 (0.87), residues: 36 loop : -0.32 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP N 29 HIS 0.009 0.001 HIS L 153 PHE 0.015 0.001 PHE L 216 TYR 0.012 0.001 TYR O 41 ARG 0.007 0.000 ARG O 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 278 time to evaluate : 2.083 Fit side-chains REVERT: L 62 GLN cc_start: 0.7776 (mt0) cc_final: 0.7455 (mt0) REVERT: L 216 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7593 (m-80) REVERT: M 93 SER cc_start: 0.8637 (p) cc_final: 0.8424 (t) REVERT: M 168 MET cc_start: 0.8445 (mmm) cc_final: 0.7841 (mmm) REVERT: M 235 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7271 (mp) REVERT: M 261 THR cc_start: 0.8348 (m) cc_final: 0.8068 (p) REVERT: M 278 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6822 (tp) REVERT: H 60 LYS cc_start: 0.6583 (mptp) cc_final: 0.6244 (mttt) REVERT: H 106 LYS cc_start: 0.7185 (mmtt) cc_final: 0.6627 (tttp) REVERT: H 130 LYS cc_start: 0.7832 (tttt) cc_final: 0.7495 (tttm) REVERT: H 177 ARG cc_start: 0.7035 (mtt-85) cc_final: 0.6290 (mtp180) REVERT: A 30 MET cc_start: 0.7507 (ttt) cc_final: 0.7099 (ttp) REVERT: B 19 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.5957 (tm-30) REVERT: I 5 TYR cc_start: 0.7494 (p90) cc_final: 0.6797 (p90) REVERT: I 10 ILE cc_start: 0.7692 (pt) cc_final: 0.7466 (pp) REVERT: I 11 PHE cc_start: 0.8057 (m-80) cc_final: 0.7659 (m-10) REVERT: I 12 ASP cc_start: 0.7554 (t70) cc_final: 0.7278 (t70) REVERT: I 15 ARG cc_start: 0.5753 (mtm110) cc_final: 0.4766 (mtt-85) REVERT: N 20 LEU cc_start: 0.7612 (tt) cc_final: 0.7401 (tt) REVERT: O 5 TYR cc_start: 0.7044 (p90) cc_final: 0.6766 (p90) REVERT: O 9 MET cc_start: 0.7572 (mtp) cc_final: 0.7336 (mtp) REVERT: O 10 ILE cc_start: 0.7497 (mt) cc_final: 0.7155 (mm) REVERT: O 20 GLN cc_start: 0.7524 (tt0) cc_final: 0.7295 (tt0) REVERT: Q 1 MET cc_start: 0.0844 (mpt) cc_final: -0.1480 (pp-130) REVERT: Q 12 ASP cc_start: 0.8020 (t0) cc_final: 0.7610 (t0) REVERT: R 18 GLN cc_start: 0.7188 (mt0) cc_final: 0.6244 (mt0) REVERT: R 25 MET cc_start: 0.8119 (mmm) cc_final: 0.7777 (mmm) REVERT: U 9 MET cc_start: 0.7199 (mtm) cc_final: 0.6604 (mtm) REVERT: V 26 SER cc_start: 0.7898 (m) cc_final: 0.7299 (t) REVERT: W 5 TYR cc_start: 0.7436 (p90) cc_final: 0.6956 (p90) REVERT: W 30 MET cc_start: 0.7648 (ttp) cc_final: 0.7398 (ttt) REVERT: W 37 SER cc_start: 0.7758 (m) cc_final: 0.7221 (p) REVERT: 2 36 ILE cc_start: 0.6255 (OUTLIER) cc_final: 0.6018 (mm) REVERT: 8 22 SER cc_start: 0.7565 (t) cc_final: 0.7207 (m) REVERT: 8 25 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7633 (mmm) REVERT: 8 36 ILE cc_start: 0.7643 (mt) cc_final: 0.7257 (mt) REVERT: 8 43 TYR cc_start: 0.7528 (t80) cc_final: 0.7174 (t80) REVERT: 9 30 MET cc_start: 0.7083 (ttm) cc_final: 0.6743 (ttm) REVERT: 0 19 GLU cc_start: 0.6256 (tp30) cc_final: 0.5804 (mm-30) REVERT: X 27 MET cc_start: 0.6365 (mtt) cc_final: 0.6057 (mtt) REVERT: Y 6 GLU cc_start: 0.5329 (tp30) cc_final: 0.5044 (tm-30) outliers start: 46 outliers final: 27 residues processed: 307 average time/residue: 1.2670 time to fit residues: 448.9782 Evaluate side-chains 300 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 267 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain 3 residue 47 SER Chi-restraints excluded: chain Z residue 20 LEU Chi-restraints excluded: chain 2 residue 36 ILE Chi-restraints excluded: chain 2 residue 37 VAL Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 7 residue 37 SER Chi-restraints excluded: chain 8 residue 25 MET Chi-restraints excluded: chain X residue 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 0.7980 chunk 125 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 215 optimal weight: 0.7980 chunk 198 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 chunk 136 optimal weight: 0.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23328 Z= 0.183 Angle : 0.954 42.445 32006 Z= 0.356 Chirality : 0.037 0.140 3105 Planarity : 0.004 0.056 3909 Dihedral : 16.192 179.593 4268 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.79 % Allowed : 15.15 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.53 (0.17), residues: 2217 helix: 2.60 (0.12), residues: 1494 sheet: -0.89 (0.88), residues: 36 loop : -0.27 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP N 29 HIS 0.011 0.001 HIS M 182 PHE 0.015 0.001 PHE H 20 TYR 0.026 0.001 TYR U 5 ARG 0.007 0.000 ARG O 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 270 time to evaluate : 2.398 Fit side-chains REVERT: L 62 GLN cc_start: 0.7839 (mt0) cc_final: 0.7469 (mt0) REVERT: L 216 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7604 (m-80) REVERT: M 93 SER cc_start: 0.8671 (p) cc_final: 0.8436 (t) REVERT: M 168 MET cc_start: 0.8423 (mmm) cc_final: 0.7820 (mmm) REVERT: M 235 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7355 (mp) REVERT: M 261 THR cc_start: 0.8346 (m) cc_final: 0.8064 (p) REVERT: M 278 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6914 (tp) REVERT: H 60 LYS cc_start: 0.6579 (mptp) cc_final: 0.6246 (mttt) REVERT: H 106 LYS cc_start: 0.7277 (mmtt) cc_final: 0.6725 (tttp) REVERT: H 130 LYS cc_start: 0.7776 (tttt) cc_final: 0.7419 (tttm) REVERT: H 177 ARG cc_start: 0.7038 (mtt-85) cc_final: 0.6287 (mtp180) REVERT: A 30 MET cc_start: 0.7549 (ttt) cc_final: 0.7161 (ttp) REVERT: B 19 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.5936 (tm-30) REVERT: I 5 TYR cc_start: 0.7466 (p90) cc_final: 0.6776 (p90) REVERT: I 10 ILE cc_start: 0.7699 (pt) cc_final: 0.7478 (pp) REVERT: I 11 PHE cc_start: 0.8069 (m-80) cc_final: 0.7663 (m-10) REVERT: I 12 ASP cc_start: 0.7558 (t70) cc_final: 0.7293 (t70) REVERT: I 15 ARG cc_start: 0.5745 (mtm110) cc_final: 0.4820 (mtt-85) REVERT: O 5 TYR cc_start: 0.7093 (p90) cc_final: 0.6815 (p90) REVERT: O 9 MET cc_start: 0.7565 (mtp) cc_final: 0.7319 (mtp) REVERT: O 10 ILE cc_start: 0.7490 (mt) cc_final: 0.7132 (mm) REVERT: Q 1 MET cc_start: 0.0694 (mpt) cc_final: -0.1513 (pp-130) REVERT: Q 12 ASP cc_start: 0.8031 (t0) cc_final: 0.7637 (t0) REVERT: R 18 GLN cc_start: 0.7180 (mt0) cc_final: 0.6292 (mt0) REVERT: R 25 MET cc_start: 0.8117 (mmm) cc_final: 0.7770 (mmm) REVERT: U 9 MET cc_start: 0.7271 (mtm) cc_final: 0.6649 (mtm) REVERT: W 30 MET cc_start: 0.7641 (ttp) cc_final: 0.7402 (ttt) REVERT: 2 36 ILE cc_start: 0.6254 (OUTLIER) cc_final: 0.6019 (mm) REVERT: 7 46 ILE cc_start: 0.4038 (OUTLIER) cc_final: 0.3767 (mp) REVERT: 8 25 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7723 (mmm) REVERT: 8 36 ILE cc_start: 0.7639 (mt) cc_final: 0.7248 (mt) REVERT: 9 30 MET cc_start: 0.7094 (ttm) cc_final: 0.6762 (ttm) REVERT: X 27 MET cc_start: 0.6300 (mtt) cc_final: 0.6015 (mtt) REVERT: Y 6 GLU cc_start: 0.5339 (tp30) cc_final: 0.5090 (tm-30) outliers start: 34 outliers final: 25 residues processed: 290 average time/residue: 1.2882 time to fit residues: 429.0190 Evaluate side-chains 299 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 267 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 278 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain Z residue 20 LEU Chi-restraints excluded: chain 2 residue 36 ILE Chi-restraints excluded: chain 2 residue 37 VAL Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 7 residue 46 ILE Chi-restraints excluded: chain 8 residue 25 MET Chi-restraints excluded: chain X residue 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 158 optimal weight: 0.4980 chunk 25 optimal weight: 7.9990 chunk 47 optimal weight: 0.0050 chunk 171 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 150 optimal weight: 20.0000 overall best weight: 2.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.123554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.098410 restraints weight = 23663.548| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.14 r_work: 0.2739 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23328 Z= 0.199 Angle : 0.961 42.564 32006 Z= 0.360 Chirality : 0.038 0.137 3105 Planarity : 0.004 0.057 3909 Dihedral : 16.167 179.579 4267 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.00 % Allowed : 14.99 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.48 (0.17), residues: 2217 helix: 2.55 (0.12), residues: 1494 sheet: -0.95 (0.87), residues: 36 loop : -0.28 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP N 29 HIS 0.012 0.001 HIS M 182 PHE 0.016 0.001 PHE H 20 TYR 0.028 0.001 TYR U 5 ARG 0.008 0.000 ARG O 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7439.01 seconds wall clock time: 133 minutes 13.81 seconds (7993.81 seconds total)