Starting phenix.real_space_refine (version: dev) on Fri Dec 16 12:12:05 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spb_10280/12_2022/6spb_10280.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spb_10280/12_2022/6spb_10280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spb_10280/12_2022/6spb_10280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spb_10280/12_2022/6spb_10280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spb_10280/12_2022/6spb_10280.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spb_10280/12_2022/6spb_10280.pdb" } resolution = 2.82 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= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "E ARG 48": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ARG 73": "NH1" <-> "NH2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ARG 85": "NH1" <-> "NH2" Residue "G ARG 148": "NH1" <-> "NH2" Residue "G ARG 159": "NH1" <-> "NH2" Residue "G ARG 166": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K ARG 104": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 45": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 52": "NH1" <-> "NH2" Residue "M ARG 56": "NH1" <-> "NH2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 90": "NH1" <-> "NH2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 101": "NH1" <-> "NH2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 54": "NH1" <-> "NH2" Residue "P ARG 63": "NH1" <-> "NH2" Residue "P ARG 90": "NH1" <-> "NH2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P ARG 110": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "R TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 11": "NH1" <-> "NH2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "T ARG 76": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "V ARG 11": "NH1" <-> "NH2" Residue "V ARG 21": "NH1" <-> "NH2" Residue "V ARG 23": "NH1" <-> "NH2" Residue "V TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W ARG 14": "NH1" <-> "NH2" Residue "W ARG 20": "NH1" <-> "NH2" Residue "W ARG 41": "NH1" <-> "NH2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 48": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "2 ARG 10": "NH1" <-> "NH2" Residue "2 ARG 16": "NH1" <-> "NH2" Residue "2 ARG 39": "NH1" <-> "NH2" Residue "2 ARG 51": "NH1" <-> "NH2" Residue "4 ARG 3": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 14": "NH1" <-> "NH2" Residue "4 ARG 19": "NH1" <-> "NH2" Residue "4 ARG 21": "NH1" <-> "NH2" Residue "4 ARG 33": "NH1" <-> "NH2" Residue "5 ARG 39": "NH1" <-> "NH2" Residue "5 ARG 41": "NH1" <-> "NH2" Residue "6 ARG 19": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 90362 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 61899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2885, 61899 Classifications: {'RNA': 2885} Modifications used: {'5*END': 1, 'rna2p_pur': 283, 'rna2p_pyr': 167, 'rna3p_pur': 1370, 'rna3p_pyr': 1065} Link IDs: {'rna2p': 450, 'rna3p': 2434} Chain breaks: 1 Chain: "B" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2495 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 54, 'rna3p_pyr': 49} Link IDs: {'rna2p': 14, 'rna3p': 102} Chain: "C" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2048 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 255} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1549 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 200} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1509 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1278 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 166} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "G" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1264 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 159} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 577 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "I" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1026 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 130} Chain: "J" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1122 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "K" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1055 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 137} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1069 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "N" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "O" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 881 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'TRANS': 114} Chain: "P" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 891 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 936 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 801 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 100} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "S" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 825 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "T" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 701 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "U" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 801 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "V" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1397 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 180} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "W" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 574 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'TRANS': 75} Chain: "X" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 626 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 468 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 58} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "Z" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 445 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "1" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 232 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "2" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 423 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "3" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 418 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "4" Number of atoms: 376 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 44, 365 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Conformer: "B" Number of residues, atoms: 44, 365 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} bond proxies already assigned to first conformer: 356 Chain: "5" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 506 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "6" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 303 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG 4 41 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG 4 41 " occ=0.50 Time building chain proxies: 38.36, per 1000 atoms: 0.42 Number of scatterers: 90362 At special positions: 0 Unit cell: (212.3, 227.7, 201.3, 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 70 16.00 P 3001 15.00 O 25492 8.00 N 16823 7.00 C 44976 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: 38.59 Conformation dependent library (CDL) restraints added in 3.5 seconds 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6148 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 47 sheets defined 24.9% alpha, 17.8% beta 933 base pairs and 1598 stacking pairs defined. Time for finding SS restraints: 31.16 Creating SS restraints... Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.590A pdb=" N ARG C 203 " --> pdb=" O HIS C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 213 removed outlier: 3.971A pdb=" N THR C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP C 213 " --> pdb=" O GLY C 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 207 through 213' Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 57 through 61 removed outlier: 3.517A pdb=" N ARG D 60 " --> pdb=" O ARG D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 72 removed outlier: 3.910A pdb=" N ALA D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.772A pdb=" N LEU D 100 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'E' and resid 23 through 37 Processing helix chain 'E' and resid 96 through 105 Processing helix chain 'E' and resid 107 through 114 Processing helix chain 'E' and resid 129 through 140 removed outlier: 3.981A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 159 Processing helix chain 'E' and resid 175 through 182 removed outlier: 3.715A pdb=" N TYR E 182 " --> pdb=" O SER E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 200 Processing helix chain 'F' and resid 11 through 20 removed outlier: 4.038A pdb=" N LYS F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU F 18 " --> pdb=" O PRO F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 62 removed outlier: 3.991A pdb=" N LYS F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE F 60 " --> pdb=" O ASP F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 101 removed outlier: 4.005A pdb=" N TYR F 97 " --> pdb=" O SER F 93 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLU F 98 " --> pdb=" O ASP F 94 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP F 101 " --> pdb=" O TYR F 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 81 removed outlier: 3.812A pdb=" N ALA G 63 " --> pdb=" O GLN G 59 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 146 Processing helix chain 'H' and resid 22 through 29 removed outlier: 3.748A pdb=" N PHE H 29 " --> pdb=" O TYR H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 48 removed outlier: 3.733A pdb=" N GLU H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 52 No H-bonds generated for 'chain 'H' and resid 50 through 52' Processing helix chain 'H' and resid 53 through 65 removed outlier: 4.445A pdb=" N ALA H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 130 Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.119A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 96 through 109 removed outlier: 4.164A pdb=" N VAL J 100 " --> pdb=" O ALA J 96 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL J 105 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 120 Processing helix chain 'K' and resid 103 through 107 removed outlier: 3.650A pdb=" N ARG K 107 " --> pdb=" O ARG K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 118 Processing helix chain 'L' and resid 37 through 41 removed outlier: 3.975A pdb=" N SER L 40 " --> pdb=" O GLY L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.582A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 98 Processing helix chain 'L' and resid 128 through 138 removed outlier: 3.567A pdb=" N ALA L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 59 removed outlier: 4.442A pdb=" N LYS M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 123 removed outlier: 3.773A pdb=" N LEU M 120 " --> pdb=" O GLU M 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 56 removed outlier: 3.551A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 68 Processing helix chain 'N' and resid 72 through 79 Processing helix chain 'O' and resid 4 through 20 removed outlier: 3.503A pdb=" N ARG O 10 " --> pdb=" O GLU O 6 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ALA O 15 " --> pdb=" O ARG O 11 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 85 removed outlier: 3.650A pdb=" N ALA O 70 " --> pdb=" O ASN O 66 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS O 71 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN O 75 " --> pdb=" O LYS O 71 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG O 80 " --> pdb=" O LEU O 76 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA O 83 " --> pdb=" O GLU O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 112 removed outlier: 3.603A pdb=" N GLY O 112 " --> pdb=" O ALA O 108 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 10 Processing helix chain 'P' and resid 54 through 57 Processing helix chain 'P' and resid 98 through 103 Processing helix chain 'Q' and resid 6 through 21 removed outlier: 3.713A pdb=" N ARG Q 11 " --> pdb=" O GLY Q 7 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 29 Processing helix chain 'Q' and resid 31 through 72 removed outlier: 4.313A pdb=" N GLN Q 37 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN Q 72 " --> pdb=" O GLY Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 86 removed outlier: 3.611A pdb=" N LYS Q 84 " --> pdb=" O ILE Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 101 Processing helix chain 'Q' and resid 102 through 116 removed outlier: 3.580A pdb=" N SER Q 116 " --> pdb=" O LYS Q 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.983A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 Processing helix chain 'S' and resid 41 through 62 removed outlier: 3.887A pdb=" N GLU S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 5 through 9 removed outlier: 3.564A pdb=" N VAL T 9 " --> pdb=" O ARG T 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 5 through 9' Processing helix chain 'T' and resid 16 through 26 Processing helix chain 'T' and resid 43 through 50 Processing helix chain 'V' and resid 15 through 25 Processing helix chain 'V' and resid 47 through 51 Processing helix chain 'V' and resid 175 through 178 Processing helix chain 'W' and resid 73 through 76 removed outlier: 3.736A pdb=" N GLY W 76 " --> pdb=" O GLY W 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 73 through 76' Processing helix chain 'X' and resid 52 through 63 Processing helix chain 'X' and resid 63 through 75 removed outlier: 3.516A pdb=" N ASP X 70 " --> pdb=" O ALA X 66 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG X 72 " --> pdb=" O LEU X 68 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA X 73 " --> pdb=" O ALA X 69 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG X 74 " --> pdb=" O ASP X 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 7 Processing helix chain 'Y' and resid 10 through 34 removed outlier: 3.574A pdb=" N SER Y 19 " --> pdb=" O GLY Y 15 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG Y 23 " --> pdb=" O SER Y 19 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP Y 24 " --> pdb=" O HIS Y 20 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 59 removed outlier: 3.857A pdb=" N SER Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS Y 47 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG Y 48 " --> pdb=" O SER Y 44 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN Y 58 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 26 Processing helix chain 'Z' and resid 40 through 50 removed outlier: 4.160A pdb=" N MET Z 46 " --> pdb=" O GLU Z 42 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 17 removed outlier: 3.569A pdb=" N ARG 2 17 " --> pdb=" O ARG 2 13 " (cutoff:3.500A) Processing helix chain '4' and resid 8 through 16 Processing helix chain '4' and resid 17 through 24 removed outlier: 4.061A pdb=" N THR 4 24 " --> pdb=" O ALA 4 20 " (cutoff:3.500A) Processing helix chain '4' and resid 24 through 37 Processing helix chain '5' and resid 7 through 12 Processing helix chain '5' and resid 36 through 42 removed outlier: 3.588A pdb=" N GLN 5 42 " --> pdb=" O LYS 5 38 " (cutoff:3.500A) Processing helix chain '5' and resid 50 through 61 removed outlier: 4.445A pdb=" N ALA 5 55 " --> pdb=" O LYS 5 51 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ARG 5 56 " --> pdb=" O SER 5 52 " (cutoff:3.500A) Processing helix chain '6' and resid 30 through 34 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.719A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LYS C 95 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N VAL C 78 " --> pdb=" O LYS C 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 131 removed outlier: 5.469A pdb=" N LEU C 164 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG C 175 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS C 183 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE C 268 " --> pdb=" O LYS C 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 144 through 145 removed outlier: 6.128A pdb=" N ILE C 144 " --> pdb=" O GLN C 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 5 through 16 removed outlier: 5.463A pdb=" N LYS D 9 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU D 29 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU D 176 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL D 107 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLU D 176 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLN D 105 " --> pdb=" O GLU D 176 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASP D 200 " --> pdb=" O GLU D 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 78 through 84 removed outlier: 5.045A pdb=" N GLY D 79 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ALA D 53 " --> pdb=" O GLY D 79 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N THR D 52 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL D 35 " --> pdb=" O THR D 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 117 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 15 through 19 removed outlier: 3.611A pdb=" N LYS G 27 " --> pdb=" O GLU G 16 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 43 through 45 removed outlier: 3.709A pdb=" N ALA G 53 " --> pdb=" O VAL G 43 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN G 45 " --> pdb=" O ARG G 51 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ARG G 51 " --> pdb=" O GLN G 45 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 83 through 88 removed outlier: 3.864A pdb=" N ARG G 85 " --> pdb=" O ILE G 129 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU G 128 " --> pdb=" O GLU G 120 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 98 through 101 removed outlier: 3.530A pdb=" N LEU G 101 " --> pdb=" O VAL G 109 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AB5, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.545A pdb=" N ILE J 54 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 74 through 77 Processing sheet with id=AB7, first strand: chain 'K' and resid 7 through 10 removed outlier: 3.863A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU K 45 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL K 19 " --> pdb=" O VAL K 43 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL K 43 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N CYS K 21 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL K 41 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS K 23 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE K 39 " --> pdb=" O LYS K 23 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ALA K 60 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU K 87 " --> pdb=" O ALA K 60 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL K 62 " --> pdb=" O VAL K 85 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL K 85 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ALA K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP K 9 " --> pdb=" O ALA K 84 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU K 86 " --> pdb=" O ASP K 9 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.670A pdb=" N ILE K 76 " --> pdb=" O THR P 74 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY P 70 " --> pdb=" O ASP K 80 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA P 59 " --> pdb=" O LYS P 51 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS P 51 " --> pdb=" O ALA P 59 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N THR P 61 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ILE P 65 " --> pdb=" O GLU P 45 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N GLU P 45 " --> pdb=" O ILE P 65 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG P 40 " --> pdb=" O VAL P 33 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE P 28 " --> pdb=" O VAL P 87 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL P 87 " --> pdb=" O ILE P 28 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLN P 30 " --> pdb=" O LEU P 85 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU P 85 " --> pdb=" O GLN P 30 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LYS P 32 " --> pdb=" O ASP P 83 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ASP P 83 " --> pdb=" O LYS P 32 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 74 through 78 removed outlier: 3.658A pdb=" N MET L 111 " --> pdb=" O VAL L 77 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 121 through 123 Processing sheet with id=AC2, first strand: chain 'M' and resid 63 through 66 removed outlier: 6.600A pdb=" N LEU M 34 " --> pdb=" O LEU M 103 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU M 105 " --> pdb=" O TYR M 32 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TYR M 32 " --> pdb=" O GLU M 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 40 through 42 removed outlier: 3.777A pdb=" N GLY M 89 " --> pdb=" O LYS M 76 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL M 74 " --> pdb=" O GLU M 91 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TRP M 93 " --> pdb=" O LYS M 72 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS M 72 " --> pdb=" O TRP M 93 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.636A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 48 through 53 removed outlier: 3.709A pdb=" N ALA O 50 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU O 27 " --> pdb=" O ASP O 92 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'R' and resid 11 through 15 removed outlier: 6.920A pdb=" N TYR R 2 " --> pdb=" O VAL R 41 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL R 41 " --> pdb=" O TYR R 2 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL R 4 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 19 through 23 removed outlier: 6.836A pdb=" N HIS R 83 " --> pdb=" O LYS R 76 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LYS R 76 " --> pdb=" O HIS R 83 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS R 85 " --> pdb=" O ILE R 74 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE R 74 " --> pdb=" O LYS R 85 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLN R 87 " --> pdb=" O VAL R 72 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL R 72 " --> pdb=" O GLN R 87 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N HIS R 89 " --> pdb=" O ASP R 70 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASP R 70 " --> pdb=" O HIS R 89 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLN R 91 " --> pdb=" O ARG R 68 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ARG R 68 " --> pdb=" O GLN R 91 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE R 93 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N HIS R 66 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'S' and resid 3 through 10 removed outlier: 5.945A pdb=" N CYS S 101 " --> pdb=" O GLY S 9 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N HIS S 102 " --> pdb=" O VAL S 76 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL S 76 " --> pdb=" O HIS S 102 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR S 104 " --> pdb=" O VAL S 74 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL S 74 " --> pdb=" O THR S 104 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS S 106 " --> pdb=" O SER S 72 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'S' and resid 82 through 87 Processing sheet with id=AD1, first strand: chain 'T' and resid 10 through 13 removed outlier: 4.155A pdb=" N LYS T 80 " --> pdb=" O VAL T 33 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'T' and resid 66 through 69 Processing sheet with id=AD3, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.017A pdb=" N GLU U 9 " --> pdb=" O PHE U 72 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE U 71 " --> pdb=" O ASP U 80 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'U' and resid 40 through 44 Processing sheet with id=AD5, first strand: chain 'U' and resid 82 through 83 Processing sheet with id=AD6, first strand: chain 'V' and resid 5 through 7 removed outlier: 6.986A pdb=" N VAL V 6 " --> pdb=" O ASN V 67 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N PHE V 94 " --> pdb=" O PRO V 30 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL V 32 " --> pdb=" O PHE V 94 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG V 96 " --> pdb=" O VAL V 32 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TYR V 34 " --> pdb=" O ARG V 96 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 81 through 82 removed outlier: 3.560A pdb=" N GLN V 81 " --> pdb=" O MET V 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'V' and resid 106 through 107 Processing sheet with id=AD9, first strand: chain 'V' and resid 126 through 127 removed outlier: 7.059A pdb=" N VAL V 160 " --> pdb=" O VAL V 184 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'W' and resid 22 through 23 removed outlier: 6.434A pdb=" N LEU W 59 " --> pdb=" O LEU W 37 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'W' and resid 30 through 31 removed outlier: 3.527A pdb=" N GLY W 65 " --> pdb=" O VAL W 31 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'W' and resid 45 through 47 removed outlier: 3.771A pdb=" N ARG W 77 " --> pdb=" O LYS W 72 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 13 through 16 Processing sheet with id=AE5, first strand: chain 'X' and resid 34 through 40 removed outlier: 3.531A pdb=" N ARG X 45 " --> pdb=" O VAL X 40 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Z' and resid 34 through 38 Processing sheet with id=AE7, first strand: chain '2' and resid 27 through 29 Processing sheet with id=AE8, first strand: chain '3' and resid 3 through 8 removed outlier: 3.541A pdb=" N THR 3 19 " --> pdb=" O ILE 3 5 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '3' and resid 33 through 36 removed outlier: 3.581A pdb=" N GLN 3 41 " --> pdb=" O ASP 3 36 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '5' and resid 15 through 17 Processing sheet with id=AF2, first strand: chain '6' and resid 14 through 19 766 hydrogen bonds defined for protein. 2106 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2349 hydrogen bonds 3648 hydrogen bond angles 0 basepair planarities 933 basepair parallelities 1598 stacking parallelities Total time for adding SS restraints: 169.44 Time building geometry restraints manager: 41.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.54: 91675 1.54 - 1.89: 6741 1.89 - 2.24: 1 2.24 - 2.60: 5 2.60 - 2.95: 1 Bond restraints: 98423 Sorted by residual: bond pdb=" CA TYR I 8 " pdb=" CB TYR I 8 " ideal model delta sigma weight residual 1.532 2.951 -1.419 1.36e-02 5.41e+03 1.09e+04 bond pdb=" N1 C A1092 " pdb=" C2 C A1092 " ideal model delta sigma weight residual 1.397 2.451 -1.054 2.00e-02 2.50e+03 2.78e+03 bond pdb=" C2 C A1092 " pdb=" N3 C A1092 " ideal model delta sigma weight residual 1.353 2.345 -0.992 2.00e-02 2.50e+03 2.46e+03 bond pdb=" N3 C A1092 " pdb=" C4 C A1092 " ideal model delta sigma weight residual 1.334 2.319 -0.985 2.00e-02 2.50e+03 2.42e+03 bond pdb=" N1 C A1092 " pdb=" C6 C A1092 " ideal model delta sigma weight residual 1.367 2.350 -0.983 2.00e-02 2.50e+03 2.41e+03 ... (remaining 98418 not shown) Histogram of bond angle deviations from ideal: 22.97 - 46.88: 1 46.88 - 70.79: 0 70.79 - 94.70: 5 94.70 - 118.61: 97179 118.61 - 142.52: 50605 Bond angle restraints: 147790 Sorted by residual: angle pdb=" O3' G A1908 " pdb=" P G A1909 " pdb=" OP1 G A1909 " ideal model delta sigma weight residual 108.00 22.97 85.03 3.00e+00 1.11e-01 8.03e+02 angle pdb=" C3' G A1908 " pdb=" O3' G A1908 " pdb=" P G A1909 " ideal model delta sigma weight residual 120.20 85.05 35.15 1.50e+00 4.44e-01 5.49e+02 angle pdb=" O3' C A1896 " pdb=" P G A1897 " pdb=" O5' G A1897 " ideal model delta sigma weight residual 104.00 138.69 -34.69 1.50e+00 4.44e-01 5.35e+02 angle pdb=" N TYR I 8 " pdb=" CA TYR I 8 " pdb=" C TYR I 8 " ideal model delta sigma weight residual 111.02 90.31 20.71 1.25e+00 6.40e-01 2.75e+02 angle pdb=" CA TYR I 8 " pdb=" CB TYR I 8 " pdb=" CG TYR I 8 " ideal model delta sigma weight residual 113.90 141.53 -27.63 1.80e+00 3.09e-01 2.36e+02 ... (remaining 147785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 49487 36.00 - 71.99: 2514 71.99 - 107.99: 166 107.99 - 143.98: 29 143.98 - 179.98: 71 Dihedral angle restraints: 52267 sinusoidal: 42704 harmonic: 9563 Sorted by residual: dihedral pdb=" CA LEU R 51 " pdb=" C LEU R 51 " pdb=" N PRO R 52 " pdb=" CA PRO R 52 " ideal model delta harmonic sigma weight residual 180.00 119.54 60.46 0 5.00e+00 4.00e-02 1.46e+02 dihedral pdb=" C TYR I 8 " pdb=" N TYR I 8 " pdb=" CA TYR I 8 " pdb=" CB TYR I 8 " ideal model delta harmonic sigma weight residual -122.60 -151.29 28.69 0 2.50e+00 1.60e-01 1.32e+02 dihedral pdb=" CA MET V 90 " pdb=" C MET V 90 " pdb=" N HIS V 91 " pdb=" CA HIS V 91 " ideal model delta harmonic sigma weight residual -180.00 -131.73 -48.27 0 5.00e+00 4.00e-02 9.32e+01 ... (remaining 52264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 18641 0.175 - 0.351: 327 0.351 - 0.526: 31 0.526 - 0.702: 3 0.702 - 0.877: 1 Chirality restraints: 19003 Sorted by residual: chirality pdb=" C1' C B 43 " pdb=" O4' C B 43 " pdb=" C2' C B 43 " pdb=" N1 C B 43 " both_signs ideal model delta sigma weight residual False 2.45 1.57 0.88 2.00e-01 2.50e+01 1.92e+01 chirality pdb=" C3' A A1627 " pdb=" C4' A A1627 " pdb=" O3' A A1627 " pdb=" C2' A A1627 " both_signs ideal model delta sigma weight residual False -2.48 -1.83 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" C3' G A2317 " pdb=" C4' G A2317 " pdb=" O3' G A2317 " pdb=" C2' G A2317 " both_signs ideal model delta sigma weight residual False -2.48 -1.92 -0.56 2.00e-01 2.50e+01 7.86e+00 ... (remaining 19000 not shown) Planarity restraints: 7570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 686 " 0.090 2.00e-02 2.50e+03 4.26e-02 5.00e+01 pdb=" N9 A A 686 " -0.101 2.00e-02 2.50e+03 pdb=" C8 A A 686 " -0.015 2.00e-02 2.50e+03 pdb=" N7 A A 686 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A A 686 " 0.017 2.00e-02 2.50e+03 pdb=" C6 A A 686 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A A 686 " 0.015 2.00e-02 2.50e+03 pdb=" N1 A A 686 " 0.014 2.00e-02 2.50e+03 pdb=" C2 A A 686 " -0.010 2.00e-02 2.50e+03 pdb=" N3 A A 686 " -0.024 2.00e-02 2.50e+03 pdb=" C4 A A 686 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 437 " -0.072 2.00e-02 2.50e+03 3.11e-02 2.89e+01 pdb=" N9 G A 437 " 0.072 2.00e-02 2.50e+03 pdb=" C8 G A 437 " 0.008 2.00e-02 2.50e+03 pdb=" N7 G A 437 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G A 437 " -0.012 2.00e-02 2.50e+03 pdb=" C6 G A 437 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G A 437 " -0.014 2.00e-02 2.50e+03 pdb=" N1 G A 437 " -0.014 2.00e-02 2.50e+03 pdb=" C2 G A 437 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G A 437 " 0.007 2.00e-02 2.50e+03 pdb=" N3 G A 437 " 0.016 2.00e-02 2.50e+03 pdb=" C4 G A 437 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 265 " 0.061 2.00e-02 2.50e+03 2.91e-02 2.33e+01 pdb=" N9 A A 265 " -0.072 2.00e-02 2.50e+03 pdb=" C8 A A 265 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A A 265 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A A 265 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A A 265 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A A 265 " 0.014 2.00e-02 2.50e+03 pdb=" N1 A A 265 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A A 265 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A A 265 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A A 265 " -0.009 2.00e-02 2.50e+03 ... (remaining 7567 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 430 2.49 - 3.09: 54813 3.09 - 3.69: 174661 3.69 - 4.30: 263552 4.30 - 4.90: 351623 Nonbonded interactions: 845079 Sorted by model distance: nonbonded pdb=" C3' G A1908 " pdb=" OP1 G A1909 " model vdw 1.887 2.776 nonbonded pdb=" OP1 U A1327 " pdb=" OH TYR T 83 " model vdw 2.182 2.440 nonbonded pdb=" O2' C A2245 " pdb=" OP2 C A2414 " model vdw 2.192 2.440 nonbonded pdb=" O2' U A2330 " pdb=" O2' A A2360 " model vdw 2.214 2.440 nonbonded pdb=" O2' G A2302 " pdb=" OG1 THR 1 24 " model vdw 2.222 2.440 ... (remaining 845074 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3001 5.49 5 S 70 5.16 5 C 44976 2.51 5 N 16823 2.21 5 O 25492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 5.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 20.930 Check model and map are aligned: 1.030 Convert atoms to be neutral: 0.590 Process input model: 343.990 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 386.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 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 : 0.015 1.419 98423 Z= 0.822 Angle : 1.306 85.027 147790 Z= 0.634 Chirality : 0.067 0.877 19003 Planarity : 0.008 0.111 7570 Dihedral : 17.703 179.976 46119 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.32 % Favored : 88.62 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 1.83 % Twisted General : 0.96 % 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: -4.29 (0.11), residues: 3326 helix: -3.28 (0.12), residues: 762 sheet: -2.19 (0.19), residues: 610 loop : -2.99 (0.11), residues: 1954 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 668 time to evaluate : 3.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 9 residues processed: 688 average time/residue: 1.8831 time to fit residues: 1706.0819 Evaluate side-chains 514 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 505 time to evaluate : 3.802 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 1 average time/residue: 1.4934 time to fit residues: 6.0875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 526 optimal weight: 5.9990 chunk 472 optimal weight: 0.9980 chunk 262 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 319 optimal weight: 0.7980 chunk 252 optimal weight: 5.9990 chunk 489 optimal weight: 6.9990 chunk 189 optimal weight: 30.0000 chunk 297 optimal weight: 3.9990 chunk 364 optimal weight: 1.9990 chunk 566 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN C 53 HIS C 153 GLN C 244 HIS C 261 ASN D 33 ASN D 105 GLN E 6 ASN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 GLN F 52 ASN F 118 ASN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN J 77 HIS J 135 GLN K 56 GLN K 89 ASN L 58 HIS L 104 HIS M 57 HIS N 9 HIS ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN P 76 GLN Q 37 GLN Q 44 GLN Q 72 ASN R 66 HIS R 82 HIS S 61 ASN S 102 HIS T 14 HIS U 2 GLN U 39 ASN U 68 ASN U 99 GLN V 83 HIS ** V 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 HIS V 178 HIS V 186 ASN W 12 ASN W 29 GLN W 35 ASN W 46 HIS Y 58 ASN Z 33 HIS 6 13 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 1.221 98423 Z= 0.309 Angle : 0.674 24.850 147790 Z= 0.349 Chirality : 0.039 0.400 19003 Planarity : 0.005 0.106 7570 Dihedral : 17.664 179.046 39749 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer Outliers : 4.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 1.83 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.13), residues: 3326 helix: -1.59 (0.17), residues: 776 sheet: -1.64 (0.19), residues: 634 loop : -2.68 (0.12), residues: 1916 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 563 time to evaluate : 4.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 119 outliers final: 44 residues processed: 631 average time/residue: 1.7863 time to fit residues: 1514.3699 Evaluate side-chains 538 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 494 time to evaluate : 3.827 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 27 residues processed: 17 average time/residue: 0.9141 time to fit residues: 29.8118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 314 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 chunk 471 optimal weight: 5.9990 chunk 385 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 567 optimal weight: 0.0170 chunk 613 optimal weight: 4.9990 chunk 505 optimal weight: 2.9990 chunk 562 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 chunk 455 optimal weight: 0.0970 overall best weight: 2.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 ASN C 200 HIS D 37 GLN D 68 HIS D 130 GLN G 107 HIS ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN K 56 GLN M 57 HIS N 22 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 HIS O 39 GLN P 39 GLN P 76 GLN Q 72 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 GLN U 99 GLN V 81 GLN ** V 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 129 HIS Y 3 ASN Y 58 ASN Z 13 ASN 2 41 HIS 3 15 HIS 4 29 GLN 6 13 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.226 98423 Z= 0.385 Angle : 0.718 22.901 147790 Z= 0.369 Chirality : 0.043 0.423 19003 Planarity : 0.006 0.105 7570 Dihedral : 17.605 179.604 39749 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer Outliers : 6.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 1.83 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.13), residues: 3326 helix: -1.11 (0.18), residues: 797 sheet: -1.50 (0.20), residues: 644 loop : -2.52 (0.12), residues: 1885 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 503 time to evaluate : 4.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 166 outliers final: 72 residues processed: 608 average time/residue: 1.7848 time to fit residues: 1460.8215 Evaluate side-chains 564 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 492 time to evaluate : 3.836 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 50 residues processed: 24 average time/residue: 0.9488 time to fit residues: 41.2266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 560 optimal weight: 0.1980 chunk 426 optimal weight: 5.9990 chunk 294 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 270 optimal weight: 3.9990 chunk 381 optimal weight: 8.9990 chunk 569 optimal weight: 8.9990 chunk 603 optimal weight: 0.8980 chunk 297 optimal weight: 6.9990 chunk 539 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 126 ASN D 140 HIS D 150 GLN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN M 57 HIS N 22 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 HIS O 39 GLN Q 72 ASN U 2 GLN U 99 GLN Y 3 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.227 98423 Z= 0.364 Angle : 0.686 21.905 147790 Z= 0.353 Chirality : 0.041 0.415 19003 Planarity : 0.005 0.106 7570 Dihedral : 17.472 179.304 39749 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer Outliers : 5.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 1.83 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.13), residues: 3326 helix: -0.71 (0.18), residues: 782 sheet: -1.45 (0.20), residues: 658 loop : -2.35 (0.13), residues: 1886 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 494 time to evaluate : 3.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 157 outliers final: 78 residues processed: 591 average time/residue: 1.7898 time to fit residues: 1427.1054 Evaluate side-chains 556 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 478 time to evaluate : 3.837 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 51 residues processed: 27 average time/residue: 0.9532 time to fit residues: 45.9080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 502 optimal weight: 4.9990 chunk 342 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 449 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 514 optimal weight: 0.6980 chunk 416 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 307 optimal weight: 3.9990 chunk 541 optimal weight: 3.9990 chunk 152 optimal weight: 20.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN D 126 ASN D 150 GLN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 HIS ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN K 29 HIS L 4 ASN L 102 ASN M 57 HIS N 22 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 HIS O 39 GLN Q 72 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 GLN U 99 GLN ** V 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 3 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.228 98423 Z= 0.374 Angle : 0.695 21.594 147790 Z= 0.357 Chirality : 0.042 0.421 19003 Planarity : 0.006 0.107 7570 Dihedral : 17.448 179.946 39749 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer Outliers : 5.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 1.83 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.13), residues: 3326 helix: -0.60 (0.18), residues: 795 sheet: -1.31 (0.21), residues: 617 loop : -2.30 (0.12), residues: 1914 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 485 time to evaluate : 3.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 157 outliers final: 85 residues processed: 585 average time/residue: 1.7619 time to fit residues: 1392.3936 Evaluate side-chains 559 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 474 time to evaluate : 3.840 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 61 residues processed: 24 average time/residue: 0.9240 time to fit residues: 40.9254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 202 optimal weight: 3.9990 chunk 543 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 354 optimal weight: 0.0270 chunk 148 optimal weight: 10.0000 chunk 603 optimal weight: 0.4980 chunk 501 optimal weight: 3.9990 chunk 279 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 316 optimal weight: 3.9990 overall best weight: 1.9044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN D 150 GLN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN L 4 ASN ** M 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 HIS O 39 GLN O 66 ASN Q 72 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 GLN U 99 GLN Y 3 ASN Y 39 GLN Y 59 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 1.228 98423 Z= 0.325 Angle : 0.664 21.481 147790 Z= 0.342 Chirality : 0.040 0.409 19003 Planarity : 0.005 0.107 7570 Dihedral : 17.421 179.626 39749 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer Outliers : 5.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 1.83 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.14), residues: 3326 helix: -0.44 (0.19), residues: 793 sheet: -1.28 (0.21), residues: 606 loop : -2.24 (0.12), residues: 1927 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 486 time to evaluate : 3.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 142 outliers final: 86 residues processed: 584 average time/residue: 1.7736 time to fit residues: 1395.1783 Evaluate side-chains 567 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 481 time to evaluate : 3.925 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 62 residues processed: 25 average time/residue: 0.9651 time to fit residues: 43.2247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 582 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 343 optimal weight: 3.9990 chunk 440 optimal weight: 3.9990 chunk 341 optimal weight: 0.6980 chunk 508 optimal weight: 1.9990 chunk 337 optimal weight: 5.9990 chunk 601 optimal weight: 3.9990 chunk 376 optimal weight: 20.0000 chunk 366 optimal weight: 0.1980 chunk 277 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN D 150 GLN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN ** M 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 HIS O 39 GLN Q 72 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 GLN U 99 GLN ** V 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 3 ASN Y 58 ASN Y 59 GLN 2 37 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 1.229 98423 Z= 0.314 Angle : 0.643 21.142 147790 Z= 0.331 Chirality : 0.039 0.404 19003 Planarity : 0.005 0.111 7570 Dihedral : 17.343 179.031 39749 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer Outliers : 5.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 1.83 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.14), residues: 3326 helix: -0.29 (0.19), residues: 786 sheet: -1.20 (0.21), residues: 616 loop : -2.16 (0.13), residues: 1924 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 479 time to evaluate : 3.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 132 outliers final: 86 residues processed: 565 average time/residue: 1.7816 time to fit residues: 1359.8958 Evaluate side-chains 555 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 469 time to evaluate : 3.811 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 63 residues processed: 24 average time/residue: 0.9930 time to fit residues: 42.1165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 372 optimal weight: 40.0000 chunk 240 optimal weight: 8.9990 chunk 359 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 382 optimal weight: 8.9990 chunk 409 optimal weight: 20.0000 chunk 297 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 472 optimal weight: 4.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 HIS D 126 ASN D 150 GLN G 81 GLN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN ** M 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 HIS O 39 GLN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 HIS U 2 GLN U 99 GLN X 16 ASN Y 3 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 1.230 98423 Z= 0.577 Angle : 0.863 21.449 147790 Z= 0.437 Chirality : 0.052 0.473 19003 Planarity : 0.007 0.118 7570 Dihedral : 17.705 179.987 39749 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer Outliers : 5.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 1.83 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.13), residues: 3326 helix: -0.75 (0.18), residues: 804 sheet: -1.28 (0.22), residues: 555 loop : -2.25 (0.12), residues: 1967 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 467 time to evaluate : 3.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 146 outliers final: 102 residues processed: 565 average time/residue: 1.8480 time to fit residues: 1410.8987 Evaluate side-chains 559 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 457 time to evaluate : 3.886 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 72 residues processed: 32 average time/residue: 1.0284 time to fit residues: 56.8458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 547 optimal weight: 5.9990 chunk 576 optimal weight: 0.9990 chunk 525 optimal weight: 0.9980 chunk 560 optimal weight: 10.0000 chunk 337 optimal weight: 0.8980 chunk 244 optimal weight: 10.0000 chunk 440 optimal weight: 0.9980 chunk 171 optimal weight: 30.0000 chunk 506 optimal weight: 2.9990 chunk 530 optimal weight: 0.9990 chunk 558 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN D 150 GLN G 81 GLN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN L 4 ASN M 57 HIS ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 HIS P 39 GLN Q 72 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 HIS R 83 HIS U 2 GLN U 99 GLN X 22 HIS Y 3 ASN Y 17 ASN Y 39 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 1.231 98423 Z= 0.267 Angle : 0.609 20.874 147790 Z= 0.312 Chirality : 0.036 0.385 19003 Planarity : 0.005 0.107 7570 Dihedral : 17.211 179.209 39749 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer Outliers : 4.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 1.83 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.14), residues: 3326 helix: -0.19 (0.19), residues: 783 sheet: -1.00 (0.22), residues: 578 loop : -2.09 (0.13), residues: 1965 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 483 time to evaluate : 3.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 109 outliers final: 66 residues processed: 560 average time/residue: 1.8135 time to fit residues: 1367.0817 Evaluate side-chains 536 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 470 time to evaluate : 3.951 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 56 residues processed: 10 average time/residue: 1.0810 time to fit residues: 21.1831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 368 optimal weight: 0.1980 chunk 592 optimal weight: 3.9990 chunk 361 optimal weight: 3.9990 chunk 281 optimal weight: 5.9990 chunk 411 optimal weight: 9.9990 chunk 621 optimal weight: 8.9990 chunk 572 optimal weight: 0.6980 chunk 495 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 382 optimal weight: 0.0270 chunk 303 optimal weight: 1.9990 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN D 150 GLN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN K 5 GLN L 4 ASN ** M 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN Q 72 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 HIS U 2 GLN U 99 GLN Y 3 ASN Y 39 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 1.233 98423 Z= 0.288 Angle : 0.617 21.024 147790 Z= 0.315 Chirality : 0.036 0.387 19003 Planarity : 0.005 0.114 7570 Dihedral : 17.086 179.783 39749 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer Outliers : 3.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 1.83 % Twisted General : 0.22 % 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: -1.97 (0.14), residues: 3326 helix: -0.08 (0.19), residues: 792 sheet: -1.02 (0.21), residues: 606 loop : -2.00 (0.13), residues: 1928 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6652 Ramachandran restraints generated. 3326 Oldfield, 0 Emsley, 3326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 484 time to evaluate : 3.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 71 residues processed: 547 average time/residue: 1.8542 time to fit residues: 1365.4354 Evaluate side-chains 549 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 478 time to evaluate : 3.896 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 56 residues processed: 15 average time/residue: 1.2468 time to fit residues: 31.9144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 393 optimal weight: 0.6980 chunk 527 optimal weight: 0.7980 chunk 151 optimal weight: 10.0000 chunk 456 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 495 optimal weight: 0.0570 chunk 207 optimal weight: 6.9990 chunk 509 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN D 150 GLN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 ASN F 118 ASN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN K 5 GLN ** M 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 HIS U 2 GLN U 99 GLN Y 3 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.157557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.131808 restraints weight = 102372.008| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 0.42 r_work: 0.3092 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 1.239 98423 Z= 0.339 Angle : 0.659 20.760 147790 Z= 0.337 Chirality : 0.039 0.405 19003 Planarity : 0.005 0.109 7570 Dihedral : 17.138 179.398 39749 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer Outliers : 3.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 1.83 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.14), residues: 3326 helix: -0.15 (0.19), residues: 797 sheet: -1.08 (0.21), residues: 608 loop : -2.01 (0.13), residues: 1921 =============================================================================== Job complete usr+sys time: 21509.09 seconds wall clock time: 378 minutes 47.12 seconds (22727.12 seconds total)