Starting phenix.real_space_refine on Sun Mar 17 00:07:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0r_22610/03_2024/7k0r_22610_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0r_22610/03_2024/7k0r_22610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0r_22610/03_2024/7k0r_22610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0r_22610/03_2024/7k0r_22610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0r_22610/03_2024/7k0r_22610_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0r_22610/03_2024/7k0r_22610_updated.pdb" } resolution = 3.3 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= 0.008 sd= 0.144 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 60 5.16 5 C 10290 2.51 5 N 2580 2.21 5 O 3096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 37": "OD1" <-> "OD2" Residue "A ASP 129": "OD1" <-> "OD2" Residue "A ASP 133": "OD1" <-> "OD2" Residue "A PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 220": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 37": "OD1" <-> "OD2" Residue "B ASP 129": "OD1" <-> "OD2" Residue "B ASP 133": "OD1" <-> "OD2" Residue "B PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 220": "OD1" <-> "OD2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 37": "OD1" <-> "OD2" Residue "C ASP 129": "OD1" <-> "OD2" Residue "C ASP 133": "OD1" <-> "OD2" Residue "C PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 220": "OD1" <-> "OD2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 37": "OD1" <-> "OD2" Residue "D ASP 129": "OD1" <-> "OD2" Residue "D ASP 133": "OD1" <-> "OD2" Residue "D PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 220": "OD1" <-> "OD2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 37": "OD1" <-> "OD2" Residue "E ASP 129": "OD1" <-> "OD2" Residue "E ASP 133": "OD1" <-> "OD2" Residue "E PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 220": "OD1" <-> "OD2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 37": "OD1" <-> "OD2" Residue "F ASP 129": "OD1" <-> "OD2" Residue "F ASP 133": "OD1" <-> "OD2" Residue "F PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 220": "OD1" <-> "OD2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2647 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 14, 'TRANS': 330} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2647 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 14, 'TRANS': 330} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2647 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 14, 'TRANS': 330} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2647 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 14, 'TRANS': 330} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "E" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2647 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 14, 'TRANS': 330} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "F" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2647 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 14, 'TRANS': 330} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'PO4': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'PO4': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'PO4': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'PO4': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'PO4': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'PO4': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Time building chain proxies: 8.78, per 1000 atoms: 0.55 Number of scatterers: 16038 At special positions: 0 Unit cell: (107.63, 106.485, 124.805, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 12 15.00 O 3096 8.00 N 2580 7.00 C 10290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.36 Conformation dependent library (CDL) restraints added in 3.0 seconds 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3876 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 36 sheets defined 22.0% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 115 through 118 No H-bonds generated for 'chain 'A' and resid 115 through 118' Processing helix chain 'A' and resid 131 through 137 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 219 through 225 Processing helix chain 'A' and resid 233 through 236 No H-bonds generated for 'chain 'A' and resid 233 through 236' Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.516A pdb=" N GLU A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 115 through 118 No H-bonds generated for 'chain 'B' and resid 115 through 118' Processing helix chain 'B' and resid 131 through 137 Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 219 through 225 Processing helix chain 'B' and resid 233 through 236 No H-bonds generated for 'chain 'B' and resid 233 through 236' Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.515A pdb=" N GLU B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 52 through 60 Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 115 through 118 No H-bonds generated for 'chain 'C' and resid 115 through 118' Processing helix chain 'C' and resid 131 through 137 Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 219 through 225 Processing helix chain 'C' and resid 233 through 236 No H-bonds generated for 'chain 'C' and resid 233 through 236' Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.515A pdb=" N GLU C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 309 Processing helix chain 'D' and resid 3 through 13 Processing helix chain 'D' and resid 52 through 60 Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'D' and resid 115 through 118 No H-bonds generated for 'chain 'D' and resid 115 through 118' Processing helix chain 'D' and resid 131 through 137 Processing helix chain 'D' and resid 209 through 216 Processing helix chain 'D' and resid 219 through 225 Processing helix chain 'D' and resid 233 through 236 No H-bonds generated for 'chain 'D' and resid 233 through 236' Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.515A pdb=" N GLU D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 309 Processing helix chain 'E' and resid 3 through 13 Processing helix chain 'E' and resid 52 through 60 Processing helix chain 'E' and resid 70 through 75 Processing helix chain 'E' and resid 115 through 118 No H-bonds generated for 'chain 'E' and resid 115 through 118' Processing helix chain 'E' and resid 131 through 137 Processing helix chain 'E' and resid 209 through 216 Processing helix chain 'E' and resid 219 through 225 Processing helix chain 'E' and resid 233 through 236 No H-bonds generated for 'chain 'E' and resid 233 through 236' Processing helix chain 'E' and resid 252 through 261 removed outlier: 3.515A pdb=" N GLU E 261 " --> pdb=" O LYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 309 Processing helix chain 'F' and resid 3 through 13 Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 70 through 75 Processing helix chain 'F' and resid 115 through 118 No H-bonds generated for 'chain 'F' and resid 115 through 118' Processing helix chain 'F' and resid 131 through 137 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 219 through 225 Processing helix chain 'F' and resid 233 through 236 No H-bonds generated for 'chain 'F' and resid 233 through 236' Processing helix chain 'F' and resid 252 through 261 removed outlier: 3.515A pdb=" N GLU F 261 " --> pdb=" O LYS F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 309 Processing sheet with id= A, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.336A pdb=" N THR A 34 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU A 42 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL A 36 " --> pdb=" O ASP A 40 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASP A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 122 through 125 removed outlier: 4.516A pdb=" N LYS A 181 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 160 through 163 Processing sheet with id= D, first strand: chain 'A' and resid 264 through 267 Processing sheet with id= E, first strand: chain 'A' and resid 276 through 279 Processing sheet with id= F, first strand: chain 'A' and resid 316 through 323 removed outlier: 5.433A pdb=" N LYS A 335 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.336A pdb=" N THR B 34 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU B 42 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL B 36 " --> pdb=" O ASP B 40 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASP B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 122 through 125 removed outlier: 4.517A pdb=" N LYS B 181 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 160 through 163 Processing sheet with id= J, first strand: chain 'B' and resid 264 through 267 Processing sheet with id= K, first strand: chain 'B' and resid 276 through 279 Processing sheet with id= L, first strand: chain 'B' and resid 316 through 323 removed outlier: 5.432A pdb=" N LYS B 335 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 25 through 28 removed outlier: 6.336A pdb=" N THR C 34 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU C 42 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL C 36 " --> pdb=" O ASP C 40 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASP C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 122 through 125 removed outlier: 4.516A pdb=" N LYS C 181 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 160 through 163 Processing sheet with id= P, first strand: chain 'C' and resid 264 through 267 Processing sheet with id= Q, first strand: chain 'C' and resid 276 through 279 Processing sheet with id= R, first strand: chain 'C' and resid 316 through 323 removed outlier: 5.433A pdb=" N LYS C 335 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL C 339 " --> pdb=" O LYS C 335 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 25 through 28 removed outlier: 6.336A pdb=" N THR D 34 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU D 42 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL D 36 " --> pdb=" O ASP D 40 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASP D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 122 through 125 removed outlier: 4.516A pdb=" N LYS D 181 " --> pdb=" O GLN D 188 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 160 through 163 Processing sheet with id= V, first strand: chain 'D' and resid 264 through 267 Processing sheet with id= W, first strand: chain 'D' and resid 276 through 279 Processing sheet with id= X, first strand: chain 'D' and resid 316 through 323 removed outlier: 5.433A pdb=" N LYS D 335 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL D 339 " --> pdb=" O LYS D 335 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 25 through 28 removed outlier: 6.337A pdb=" N THR E 34 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU E 42 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL E 36 " --> pdb=" O ASP E 40 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASP E 40 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 122 through 125 removed outlier: 4.517A pdb=" N LYS E 181 " --> pdb=" O GLN E 188 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 160 through 163 Processing sheet with id= AB, first strand: chain 'E' and resid 264 through 267 Processing sheet with id= AC, first strand: chain 'E' and resid 276 through 279 Processing sheet with id= AD, first strand: chain 'E' and resid 316 through 323 removed outlier: 5.433A pdb=" N LYS E 335 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL E 339 " --> pdb=" O LYS E 335 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 25 through 28 removed outlier: 6.336A pdb=" N THR F 34 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU F 42 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL F 36 " --> pdb=" O ASP F 40 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASP F 40 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 122 through 125 removed outlier: 4.517A pdb=" N LYS F 181 " --> pdb=" O GLN F 188 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 160 through 163 Processing sheet with id= AH, first strand: chain 'F' and resid 264 through 267 Processing sheet with id= AI, first strand: chain 'F' and resid 276 through 279 Processing sheet with id= AJ, first strand: chain 'F' and resid 316 through 323 removed outlier: 5.433A pdb=" N LYS F 335 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL F 339 " --> pdb=" O LYS F 335 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1242 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: 4.65 Time building geometry restraints manager: 6.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5106 1.33 - 1.45: 2192 1.45 - 1.57: 8980 1.57 - 1.68: 6 1.68 - 1.80: 90 Bond restraints: 16374 Sorted by residual: bond pdb=" O3 PO4 D 402 " pdb=" P PO4 D 402 " ideal model delta sigma weight residual 1.569 1.504 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" O3 PO4 F 402 " pdb=" P PO4 F 402 " ideal model delta sigma weight residual 1.569 1.505 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O3 PO4 E 402 " pdb=" P PO4 E 402 " ideal model delta sigma weight residual 1.569 1.505 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O3 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.75e+00 bond pdb=" O3 PO4 A 402 " pdb=" P PO4 A 402 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.63e+00 ... (remaining 16369 not shown) Histogram of bond angle deviations from ideal: 100.49 - 107.17: 560 107.17 - 113.85: 9466 113.85 - 120.54: 6258 120.54 - 127.22: 5910 127.22 - 133.90: 144 Bond angle restraints: 22338 Sorted by residual: angle pdb=" O1P U5P B 401 " pdb=" P U5P B 401 " pdb=" O2P U5P B 401 " ideal model delta sigma weight residual 119.60 111.25 8.35 3.00e+00 1.11e-01 7.75e+00 angle pdb=" O1P U5P C 401 " pdb=" P U5P C 401 " pdb=" O2P U5P C 401 " ideal model delta sigma weight residual 119.60 111.29 8.31 3.00e+00 1.11e-01 7.68e+00 angle pdb=" O1P U5P A 401 " pdb=" P U5P A 401 " pdb=" O2P U5P A 401 " ideal model delta sigma weight residual 119.60 111.29 8.31 3.00e+00 1.11e-01 7.68e+00 angle pdb=" CA TYR A 231 " pdb=" CB TYR A 231 " pdb=" CG TYR A 231 " ideal model delta sigma weight residual 113.90 109.32 4.58 1.80e+00 3.09e-01 6.46e+00 angle pdb=" CA TYR B 231 " pdb=" CB TYR B 231 " pdb=" CG TYR B 231 " ideal model delta sigma weight residual 113.90 109.35 4.55 1.80e+00 3.09e-01 6.38e+00 ... (remaining 22333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 8934 17.06 - 34.12: 576 34.12 - 51.19: 114 51.19 - 68.25: 72 68.25 - 85.31: 30 Dihedral angle restraints: 9726 sinusoidal: 3720 harmonic: 6006 Sorted by residual: dihedral pdb=" CA PHE A 177 " pdb=" C PHE A 177 " pdb=" N ASN A 178 " pdb=" CA ASN A 178 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA PHE E 177 " pdb=" C PHE E 177 " pdb=" N ASN E 178 " pdb=" CA ASN E 178 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA PHE D 177 " pdb=" C PHE D 177 " pdb=" N ASN D 178 " pdb=" CA ASN D 178 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 9723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1261 0.032 - 0.063: 726 0.063 - 0.095: 398 0.095 - 0.127: 168 0.127 - 0.158: 69 Chirality restraints: 2622 Sorted by residual: chirality pdb=" CA ILE A 80 " pdb=" N ILE A 80 " pdb=" C ILE A 80 " pdb=" CB ILE A 80 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CB ILE B 28 " pdb=" CA ILE B 28 " pdb=" CG1 ILE B 28 " pdb=" CG2 ILE B 28 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA ILE F 169 " pdb=" N ILE F 169 " pdb=" C ILE F 169 " pdb=" CB ILE F 169 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.92e-01 ... (remaining 2619 not shown) Planarity restraints: 2856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 59 " -0.010 2.00e-02 2.50e+03 1.05e-02 2.78e+00 pdb=" CG TRP C 59 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP C 59 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP C 59 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 59 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 59 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 59 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 59 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 59 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 59 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 59 " -0.010 2.00e-02 2.50e+03 1.05e-02 2.73e+00 pdb=" CG TRP B 59 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP B 59 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 59 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 59 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 59 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 59 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 59 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 59 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 59 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 59 " 0.010 2.00e-02 2.50e+03 1.04e-02 2.72e+00 pdb=" CG TRP D 59 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP D 59 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP D 59 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 59 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 59 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 59 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 59 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 59 " 0.001 2.00e-02 2.50e+03 ... (remaining 2853 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 373 2.68 - 3.23: 15800 3.23 - 3.79: 26706 3.79 - 4.34: 35480 4.34 - 4.90: 58731 Nonbonded interactions: 137090 Sorted by model distance: nonbonded pdb=" NE2 HIS A 235 " pdb=" O1 PO4 A 402 " model vdw 2.122 2.520 nonbonded pdb=" NE2 HIS E 235 " pdb=" O3 PO4 E 402 " model vdw 2.122 2.520 nonbonded pdb=" NE2 HIS D 235 " pdb=" O3 PO4 D 402 " model vdw 2.122 2.520 nonbonded pdb=" NE2 HIS B 235 " pdb=" O1 PO4 B 402 " model vdw 2.122 2.520 nonbonded pdb=" NE2 HIS C 235 " pdb=" O1 PO4 C 402 " model vdw 2.122 2.520 ... (remaining 137085 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.380 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 44.530 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 0.010 0.065 16374 Z= 0.640 Angle : 0.786 8.353 22338 Z= 0.434 Chirality : 0.054 0.158 2622 Planarity : 0.004 0.030 2856 Dihedral : 14.417 85.311 5850 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.05 % Allowed : 4.21 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.16), residues: 2058 helix: -1.17 (0.19), residues: 534 sheet: -0.50 (0.26), residues: 336 loop : -0.46 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 59 HIS 0.008 0.002 HIS E 96 PHE 0.026 0.003 PHE D 177 TYR 0.025 0.003 TYR B 231 ARG 0.005 0.001 ARG F 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 1.823 Fit side-chains REVERT: A 68 PRO cc_start: 0.8223 (Cg_exo) cc_final: 0.7961 (Cg_endo) REVERT: B 245 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7645 (tp40) REVERT: B 331 MET cc_start: 0.6147 (mmm) cc_final: 0.5912 (tpt) REVERT: C 219 MET cc_start: 0.8251 (ttp) cc_final: 0.7654 (ttm) REVERT: E 245 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.7183 (tp40) outliers start: 18 outliers final: 2 residues processed: 137 average time/residue: 0.2739 time to fit residues: 57.3415 Evaluate side-chains 60 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 245 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16374 Z= 0.178 Angle : 0.495 6.264 22338 Z= 0.269 Chirality : 0.045 0.163 2622 Planarity : 0.003 0.033 2856 Dihedral : 9.807 61.174 2330 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 1.40 % Allowed : 7.19 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.17), residues: 2058 helix: 0.29 (0.23), residues: 540 sheet: 0.62 (0.25), residues: 330 loop : -0.16 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 333 HIS 0.004 0.001 HIS D 235 PHE 0.009 0.001 PHE A 135 TYR 0.021 0.002 TYR D 33 ARG 0.005 0.001 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 69 time to evaluate : 1.985 Fit side-chains revert: symmetry clash REVERT: A 68 PRO cc_start: 0.8527 (Cg_exo) cc_final: 0.8305 (Cg_endo) REVERT: B 331 MET cc_start: 0.6319 (mmm) cc_final: 0.5951 (tpp) outliers start: 24 outliers final: 12 residues processed: 89 average time/residue: 0.2665 time to fit residues: 37.2788 Evaluate side-chains 64 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 314 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 185 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 165 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN B 29 ASN D 29 ASN F 29 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16374 Z= 0.412 Angle : 0.627 12.732 22338 Z= 0.333 Chirality : 0.048 0.180 2622 Planarity : 0.004 0.027 2856 Dihedral : 9.662 60.830 2324 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.52 % Allowed : 8.19 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.17), residues: 2058 helix: 0.12 (0.22), residues: 534 sheet: 0.19 (0.25), residues: 372 loop : -0.06 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 333 HIS 0.006 0.002 HIS A 96 PHE 0.014 0.002 PHE A 269 TYR 0.021 0.002 TYR A 33 ARG 0.010 0.001 ARG E 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 50 time to evaluate : 1.805 Fit side-chains REVERT: B 210 MET cc_start: 0.7219 (ttm) cc_final: 0.6997 (ttm) REVERT: B 331 MET cc_start: 0.6905 (mmm) cc_final: 0.6320 (tpt) REVERT: C 219 MET cc_start: 0.8352 (ttp) cc_final: 0.7941 (ttm) REVERT: F 186 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8451 (m) outliers start: 26 outliers final: 14 residues processed: 71 average time/residue: 0.2329 time to fit residues: 28.4008 Evaluate side-chains 58 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 43 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 243 HIS Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain F residue 186 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 0.0670 chunk 124 optimal weight: 0.7980 chunk 186 optimal weight: 7.9990 chunk 197 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 176 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 overall best weight: 1.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16374 Z= 0.184 Angle : 0.454 7.574 22338 Z= 0.245 Chirality : 0.044 0.159 2622 Planarity : 0.003 0.029 2856 Dihedral : 9.449 61.108 2322 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.35 % Allowed : 8.77 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.18), residues: 2058 helix: 0.52 (0.23), residues: 534 sheet: 0.99 (0.29), residues: 324 loop : -0.03 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 333 HIS 0.004 0.001 HIS E 250 PHE 0.008 0.001 PHE B 44 TYR 0.014 0.001 TYR E 238 ARG 0.004 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 46 time to evaluate : 1.722 Fit side-chains revert: symmetry clash REVERT: B 331 MET cc_start: 0.6860 (mmm) cc_final: 0.6551 (tpp) REVERT: F 186 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8641 (m) outliers start: 23 outliers final: 12 residues processed: 68 average time/residue: 0.2168 time to fit residues: 25.7528 Evaluate side-chains 55 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 220 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 146 optimal weight: 0.0670 chunk 81 optimal weight: 3.9990 chunk 168 optimal weight: 0.1980 chunk 136 optimal weight: 6.9990 chunk 0 optimal weight: 0.7980 chunk 100 optimal weight: 0.0370 chunk 176 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 16374 Z= 0.141 Angle : 0.418 4.448 22338 Z= 0.226 Chirality : 0.044 0.153 2622 Planarity : 0.003 0.029 2856 Dihedral : 9.256 61.002 2322 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.29 % Allowed : 9.53 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.18), residues: 2058 helix: 0.69 (0.23), residues: 540 sheet: 1.26 (0.29), residues: 324 loop : 0.13 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 333 HIS 0.004 0.001 HIS E 250 PHE 0.008 0.001 PHE A 303 TYR 0.014 0.001 TYR D 33 ARG 0.004 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 43 time to evaluate : 1.990 Fit side-chains REVERT: C 331 MET cc_start: 0.6898 (tpp) cc_final: 0.6629 (tpp) REVERT: F 186 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8429 (p) REVERT: F 331 MET cc_start: 0.6815 (mmm) cc_final: 0.6364 (tpp) outliers start: 22 outliers final: 13 residues processed: 65 average time/residue: 0.2461 time to fit residues: 27.4134 Evaluate side-chains 57 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 43 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 220 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 3.9990 chunk 177 optimal weight: 0.0270 chunk 38 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 65 optimal weight: 0.0070 chunk 103 optimal weight: 6.9990 overall best weight: 1.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.6240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16374 Z= 0.207 Angle : 0.448 5.220 22338 Z= 0.239 Chirality : 0.044 0.152 2622 Planarity : 0.003 0.027 2856 Dihedral : 9.284 61.139 2322 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.23 % Allowed : 9.77 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.18), residues: 2058 helix: 0.60 (0.23), residues: 540 sheet: 1.28 (0.30), residues: 324 loop : 0.12 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 333 HIS 0.004 0.001 HIS E 250 PHE 0.009 0.001 PHE A 269 TYR 0.014 0.001 TYR A 33 ARG 0.004 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 43 time to evaluate : 1.901 Fit side-chains REVERT: B 331 MET cc_start: 0.7057 (tpp) cc_final: 0.6750 (tpp) REVERT: C 210 MET cc_start: 0.7894 (ttm) cc_final: 0.7641 (ttm) REVERT: F 186 VAL cc_start: 0.9000 (OUTLIER) cc_final: 0.8556 (p) REVERT: F 331 MET cc_start: 0.6855 (mmm) cc_final: 0.6350 (tpt) outliers start: 21 outliers final: 18 residues processed: 63 average time/residue: 0.2303 time to fit residues: 25.8155 Evaluate side-chains 60 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 41 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 220 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.6407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16374 Z= 0.148 Angle : 0.415 4.551 22338 Z= 0.223 Chirality : 0.044 0.149 2622 Planarity : 0.003 0.029 2856 Dihedral : 9.227 61.078 2322 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.17 % Allowed : 10.12 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.19), residues: 2058 helix: 0.65 (0.23), residues: 540 sheet: 1.33 (0.30), residues: 324 loop : 0.21 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 333 HIS 0.003 0.001 HIS E 250 PHE 0.007 0.001 PHE F 330 TYR 0.013 0.001 TYR C 33 ARG 0.004 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 43 time to evaluate : 1.869 Fit side-chains REVERT: B 331 MET cc_start: 0.7000 (tpp) cc_final: 0.6662 (tpp) REVERT: F 331 MET cc_start: 0.6865 (mmm) cc_final: 0.6335 (tpt) outliers start: 20 outliers final: 17 residues processed: 62 average time/residue: 0.2213 time to fit residues: 24.3244 Evaluate side-chains 58 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 41 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 220 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.0970 chunk 78 optimal weight: 0.1980 chunk 117 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 133 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.6666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 16374 Z= 0.186 Angle : 0.432 4.851 22338 Z= 0.232 Chirality : 0.044 0.150 2622 Planarity : 0.003 0.027 2856 Dihedral : 9.228 61.037 2322 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.35 % Allowed : 9.94 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.19), residues: 2058 helix: 0.67 (0.23), residues: 534 sheet: 1.31 (0.30), residues: 324 loop : 0.23 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 333 HIS 0.003 0.001 HIS B 96 PHE 0.009 0.001 PHE A 269 TYR 0.014 0.001 TYR D 33 ARG 0.004 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 44 time to evaluate : 1.852 Fit side-chains REVERT: A 105 MET cc_start: 0.7392 (mtt) cc_final: 0.7080 (mtt) REVERT: B 331 MET cc_start: 0.7035 (tpp) cc_final: 0.6706 (tpp) REVERT: F 331 MET cc_start: 0.6878 (mmm) cc_final: 0.6385 (tpt) outliers start: 23 outliers final: 19 residues processed: 66 average time/residue: 0.2189 time to fit residues: 25.3495 Evaluate side-chains 61 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 42 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 220 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 110 optimal weight: 0.0070 chunk 79 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 56 optimal weight: 8.9990 chunk 165 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.6772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 16374 Z= 0.125 Angle : 0.404 5.007 22338 Z= 0.218 Chirality : 0.043 0.146 2622 Planarity : 0.003 0.029 2856 Dihedral : 9.180 61.054 2322 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.29 % Allowed : 10.18 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.19), residues: 2058 helix: 0.74 (0.24), residues: 534 sheet: 1.39 (0.30), residues: 324 loop : 0.31 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 333 HIS 0.002 0.001 HIS E 250 PHE 0.007 0.001 PHE F 330 TYR 0.012 0.001 TYR D 33 ARG 0.004 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 45 time to evaluate : 1.933 Fit side-chains REVERT: A 105 MET cc_start: 0.7366 (mtt) cc_final: 0.7001 (mtt) REVERT: B 331 MET cc_start: 0.7034 (tpp) cc_final: 0.6710 (tpp) REVERT: F 331 MET cc_start: 0.6860 (mmm) cc_final: 0.6501 (tpt) outliers start: 22 outliers final: 14 residues processed: 66 average time/residue: 0.2530 time to fit residues: 27.8892 Evaluate side-chains 56 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 0.5980 chunk 118 optimal weight: 0.3980 chunk 91 optimal weight: 8.9990 chunk 134 optimal weight: 0.7980 chunk 203 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 128 optimal weight: 0.0170 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.6853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16374 Z= 0.113 Angle : 0.406 6.981 22338 Z= 0.217 Chirality : 0.043 0.146 2622 Planarity : 0.003 0.028 2856 Dihedral : 9.137 60.957 2322 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.88 % Allowed : 10.64 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.19), residues: 2058 helix: 0.75 (0.24), residues: 534 sheet: 1.64 (0.30), residues: 312 loop : 0.36 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP A 333 HIS 0.002 0.001 HIS E 250 PHE 0.006 0.001 PHE F 330 TYR 0.013 0.001 TYR D 33 ARG 0.005 0.000 ARG B 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 46 time to evaluate : 1.786 Fit side-chains REVERT: A 105 MET cc_start: 0.7396 (mtt) cc_final: 0.7079 (mtt) REVERT: B 272 MET cc_start: 0.8025 (ptt) cc_final: 0.7803 (ptm) REVERT: B 331 MET cc_start: 0.7028 (tpp) cc_final: 0.6711 (tpp) REVERT: F 331 MET cc_start: 0.6888 (mmm) cc_final: 0.6651 (tpp) outliers start: 15 outliers final: 14 residues processed: 60 average time/residue: 0.2048 time to fit residues: 23.0324 Evaluate side-chains 56 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 162 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 166 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 142 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.062087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.053010 restraints weight = 60861.185| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.89 r_work: 0.3135 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.6927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 16374 Z= 0.114 Angle : 0.404 5.538 22338 Z= 0.216 Chirality : 0.043 0.146 2622 Planarity : 0.003 0.027 2856 Dihedral : 9.125 60.968 2322 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.05 % Allowed : 10.53 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.19), residues: 2058 helix: 0.79 (0.24), residues: 534 sheet: 1.68 (0.30), residues: 312 loop : 0.39 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 333 HIS 0.002 0.001 HIS E 250 PHE 0.006 0.001 PHE F 330 TYR 0.013 0.001 TYR D 33 ARG 0.005 0.000 ARG B 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2498.33 seconds wall clock time: 46 minutes 49.53 seconds (2809.53 seconds total)