Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 23:01:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0r_22610/04_2023/7k0r_22610_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0r_22610/04_2023/7k0r_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_22610/04_2023/7k0r_22610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0r_22610/04_2023/7k0r_22610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0r_22610/04_2023/7k0r_22610_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0r_22610/04_2023/7k0r_22610_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 8.42, per 1000 atoms: 0.53 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: 6.30 Conformation dependent library (CDL) restraints added in 2.3 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: 1.57 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: 4.61 Time building geometry restraints manager: 6.74 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: 8916 17.06 - 34.12: 504 34.12 - 51.19: 114 51.19 - 68.25: 30 68.25 - 85.31: 30 Dihedral angle restraints: 9594 sinusoidal: 3588 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 9591 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: 0.810 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: 4.790 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 41.730 Find NCS groups from input model: 1.050 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.590 ------------------------------------------------------------------------------- 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 : 13.366 85.311 5718 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 % 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 *********************** 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 : 2.104 Fit side-chains outliers start: 18 outliers final: 2 residues processed: 137 average time/residue: 0.2795 time to fit residues: 58.6230 Evaluate side-chains 58 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 1.940 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1390 time to fit residues: 3.1025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7618 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 16374 Z= 0.181 Angle : 0.494 5.542 22338 Z= 0.266 Chirality : 0.045 0.173 2622 Planarity : 0.003 0.034 2856 Dihedral : 4.671 18.711 2190 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer Outliers : 1.17 % 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: 0.10 (0.17), residues: 2058 helix: 0.37 (0.23), residues: 534 sheet: 0.61 (0.25), residues: 330 loop : -0.15 (0.17), residues: 1194 *********************** 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 88 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 68 time to evaluate : 1.868 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 84 average time/residue: 0.2796 time to fit residues: 37.2391 Evaluate side-chains 61 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 1.984 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1423 time to fit residues: 5.3255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 185 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 184 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 E 29 ASN F 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 16374 Z= 0.391 Angle : 0.654 13.073 22338 Z= 0.345 Chirality : 0.049 0.196 2622 Planarity : 0.004 0.029 2856 Dihedral : 5.169 20.372 2190 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 1.29 % 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: -0.05 (0.17), residues: 2058 helix: 0.17 (0.22), residues: 528 sheet: 0.16 (0.25), residues: 372 loop : -0.08 (0.17), residues: 1158 *********************** 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 71 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 49 time to evaluate : 1.992 Fit side-chains outliers start: 22 outliers final: 10 residues processed: 67 average time/residue: 0.2574 time to fit residues: 29.1461 Evaluate side-chains 53 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 2.065 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1476 time to fit residues: 5.5148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 186 optimal weight: 7.9990 chunk 197 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 176 optimal weight: 0.0670 chunk 53 optimal weight: 3.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- 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: 0.8063 moved from start: 0.6014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 16374 Z= 0.149 Angle : 0.449 7.482 22338 Z= 0.241 Chirality : 0.044 0.157 2622 Planarity : 0.003 0.028 2856 Dihedral : 4.529 18.757 2190 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer Outliers : 0.82 % 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: 0.38 (0.18), residues: 2058 helix: 0.52 (0.23), residues: 534 sheet: 1.02 (0.29), residues: 324 loop : -0.01 (0.17), residues: 1200 *********************** 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 59 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 45 time to evaluate : 1.925 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 57 average time/residue: 0.2805 time to fit residues: 26.5729 Evaluate side-chains 46 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 2.033 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1479 time to fit residues: 3.6768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 81 optimal weight: 2.9990 chunk 168 optimal weight: 0.0070 chunk 136 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 overall best weight: 2.3604 ------------------------------------------------------------------------------- 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: 0.8109 moved from start: 0.6361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 16374 Z= 0.263 Angle : 0.485 6.552 22338 Z= 0.256 Chirality : 0.045 0.158 2622 Planarity : 0.003 0.028 2856 Dihedral : 4.527 17.806 2190 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 0.64 % 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: 0.46 (0.23), residues: 534 sheet: 1.06 (0.30), residues: 324 loop : -0.02 (0.17), residues: 1200 *********************** 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 53 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 2.094 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 51 average time/residue: 0.2962 time to fit residues: 25.0505 Evaluate side-chains 48 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 1.919 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1484 time to fit residues: 4.5013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 38 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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: 0.8099 moved from start: 0.6549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 16374 Z= 0.201 Angle : 0.448 6.689 22338 Z= 0.238 Chirality : 0.044 0.151 2622 Planarity : 0.003 0.029 2856 Dihedral : 4.376 19.367 2190 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer Outliers : 0.18 % 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: 0.43 (0.18), residues: 2058 helix: 0.48 (0.23), residues: 534 sheet: 1.12 (0.30), residues: 324 loop : 0.05 (0.18), residues: 1200 *********************** 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 44 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 1.872 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 44 average time/residue: 0.2869 time to fit residues: 21.6051 Evaluate side-chains 41 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 2.016 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 144 optimal weight: 0.0770 chunk 111 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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: 0.6655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 16374 Z= 0.113 Angle : 0.415 6.670 22338 Z= 0.222 Chirality : 0.043 0.145 2622 Planarity : 0.003 0.029 2856 Dihedral : 4.118 18.692 2190 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer Outliers : 0.47 % 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: 0.64 (0.19), residues: 2058 helix: 0.64 (0.23), residues: 534 sheet: 1.25 (0.30), residues: 324 loop : 0.19 (0.18), residues: 1200 *********************** 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 55 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 2.075 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 54 average time/residue: 0.2873 time to fit residues: 25.8597 Evaluate side-chains 45 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 2.160 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1501 time to fit residues: 3.3442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.6887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.040 16374 Z= 0.376 Angle : 0.540 7.881 22338 Z= 0.282 Chirality : 0.047 0.160 2622 Planarity : 0.003 0.028 2856 Dihedral : 4.569 17.596 2190 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 0.53 % 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: 0.22 (0.19), residues: 2058 helix: 0.26 (0.23), residues: 534 sheet: 0.57 (0.29), residues: 360 loop : 0.06 (0.18), residues: 1164 *********************** 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 49 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 1.967 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 48 average time/residue: 0.2261 time to fit residues: 20.1624 Evaluate side-chains 43 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 1.956 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1551 time to fit residues: 3.7902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 79 optimal weight: 0.0000 chunk 143 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 165 optimal weight: 9.9990 chunk 173 optimal weight: 0.9990 chunk 182 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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: 0.8084 moved from start: 0.6958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 16374 Z= 0.118 Angle : 0.428 6.732 22338 Z= 0.228 Chirality : 0.043 0.144 2622 Planarity : 0.003 0.029 2856 Dihedral : 4.197 19.404 2190 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer Outliers : 0.23 % 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 (0.19), residues: 2058 helix: 0.52 (0.23), residues: 534 sheet: 1.42 (0.31), residues: 312 loop : 0.19 (0.18), residues: 1212 *********************** 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 45 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 2.358 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 44 average time/residue: 0.2760 time to fit residues: 20.8473 Evaluate side-chains 43 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 1.951 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1483 time to fit residues: 3.0495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 134 optimal weight: 0.6980 chunk 203 optimal weight: 10.0000 chunk 187 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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: 0.8123 moved from start: 0.7052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 16374 Z= 0.269 Angle : 0.481 8.380 22338 Z= 0.253 Chirality : 0.045 0.152 2622 Planarity : 0.003 0.029 2856 Dihedral : 4.360 17.691 2190 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 2058 helix: 0.37 (0.23), residues: 534 sheet: 1.01 (0.31), residues: 330 loop : 0.13 (0.18), residues: 1194 ********************** 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 40 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.858 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.2455 time to fit residues: 17.5615 Evaluate side-chains 40 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.739 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.061437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.052313 restraints weight = 61519.031| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.91 r_work: 0.3112 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.7112 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= 0.122 Angle : 0.423 7.088 22338 Z= 0.225 Chirality : 0.044 0.145 2622 Planarity : 0.003 0.028 2856 Dihedral : 4.132 18.201 2190 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer Outliers : 0.06 % 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: 0.69 (0.19), residues: 2058 helix: 0.52 (0.23), residues: 534 sheet: 1.47 (0.31), residues: 312 loop : 0.26 (0.18), residues: 1212 =============================================================================== Job complete usr+sys time: 2250.05 seconds wall clock time: 42 minutes 47.51 seconds (2567.51 seconds total)