Starting phenix.real_space_refine (version: dev) on Sat Dec 17 08:59:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7teo_25848/12_2022/7teo_25848.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7teo_25848/12_2022/7teo_25848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7teo_25848/12_2022/7teo_25848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7teo_25848/12_2022/7teo_25848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7teo_25848/12_2022/7teo_25848.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7teo_25848/12_2022/7teo_25848.pdb" } resolution = 2.97 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= 0.002 sd= 0.115 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 "2 GLU 121": "OE1" <-> "OE2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 207": "OD1" <-> "OD2" Residue "D ASP 68": "OD1" <-> "OD2" Residue "D ASP 142": "OD1" <-> "OD2" Residue "D ASP 180": "OD1" <-> "OD2" Residue "D TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 71": "OD1" <-> "OD2" Residue "E PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "G ASP 17": "OD1" <-> "OD2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H ASP 123": "OD1" <-> "OD2" Residue "H GLU 169": "OE1" <-> "OE2" Residue "I TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 179": "OE1" <-> "OE2" Residue "I ASP 212": "OD1" <-> "OD2" Residue "I GLU 227": "OE1" <-> "OE2" Residue "J ASP 144": "OD1" <-> "OD2" Residue "K GLU 49": "OE1" <-> "OE2" Residue "K GLU 58": "OE1" <-> "OE2" Residue "K GLU 87": "OE1" <-> "OE2" Residue "K TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 169": "OE1" <-> "OE2" Residue "L ASP 92": "OD1" <-> "OD2" Residue "L GLU 147": "OE1" <-> "OE2" Residue "L GLU 257": "OE1" <-> "OE2" Residue "L ASP 267": "OD1" <-> "OD2" Residue "M ASP 45": "OD1" <-> "OD2" Residue "M PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 87": "OD1" <-> "OD2" Residue "Q GLU 237": "OE1" <-> "OE2" Residue "R TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 180": "OD1" <-> "OD2" Residue "S PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 110": "OE1" <-> "OE2" Residue "T TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U ASP 233": "OD1" <-> "OD2" Residue "U ASP 240": "OD1" <-> "OD2" Residue "V GLU 83": "OE1" <-> "OE2" Residue "W GLU 93": "OE1" <-> "OE2" Residue "W TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W GLU 179": "OE1" <-> "OE2" Residue "W ASP 212": "OD1" <-> "OD2" Residue "X GLU 65": "OE1" <-> "OE2" Residue "X ASP 178": "OD1" <-> "OD2" Residue "Y ASP 72": "OD1" <-> "OD2" Residue "Y GLU 155": "OE1" <-> "OE2" Residue "Y GLU 169": "OE1" <-> "OE2" Residue "Z GLU 111": "OE1" <-> "OE2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "Z GLU 145": "OE1" <-> "OE2" Residue "Z TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z GLU 257": "OE1" <-> "OE2" Residue "Z ASP 267": "OD1" <-> "OD2" Residue "a GLU 132": "OE1" <-> "OE2" Residue "a ASP 201": "OD1" <-> "OD2" Residue "a PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 132": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 97522 Number of models: 1 Model: "" Number of chains: 30 Chain: "1" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3449 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 213} Chain: "2" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3595 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 8, 'TRANS': 221} Chain: "A" Number of atoms: 3687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3687 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 3694 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "C" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3521 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain breaks: 4 Chain: "D" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3288 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 8, 'TRANS': 199} Chain breaks: 2 Chain: "E" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3176 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 3, 'TRANS': 203} Chain breaks: 2 Chain: "F" Number of atoms: 3551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3551 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain: "G" Number of atoms: 3776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 3776 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain: "H" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 2992 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "I" Number of atoms: 3347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3347 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain: "J" Number of atoms: 3142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3142 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "K" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3130 Classifications: {'peptide': 195} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "L" Number of atoms: 3237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3237 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 209} Chain: "M" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3449 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 213} Chain: "N" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3595 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 8, 'TRANS': 221} Chain: "O" Number of atoms: 3687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3687 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Chain: "P" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 3694 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "Q" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3521 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain breaks: 4 Chain: "R" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3287 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 8, 'TRANS': 199} Chain breaks: 2 Chain: "S" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3176 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 3, 'TRANS': 203} Chain breaks: 2 Chain: "T" Number of atoms: 3551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3551 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain: "U" Number of atoms: 3776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 3776 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain: "V" Number of atoms: 2991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 2991 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "W" Number of atoms: 3347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3347 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain: "X" Number of atoms: 3142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3142 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "Y" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3130 Classifications: {'peptide': 195} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "Z" Number of atoms: 3237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3237 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 209} Chain: "a" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1177 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 14, 'TRANS': 66} Chain breaks: 3 Chain: "b" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1177 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 14, 'TRANS': 66} Chain breaks: 3 Time building chain proxies: 34.20, per 1000 atoms: 0.35 Number of scatterers: 97522 At special positions: 0 Unit cell: (187.62, 198.22, 144.16, 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 162 16.00 O 9492 8.00 N 8304 7.00 C 30952 6.00 H 48612 1.00 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: 74.62 Conformation dependent library (CDL) restraints added in 6.9 seconds 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11564 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 72 sheets defined 40.1% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain '1' and resid 76 through 98 Processing helix chain '1' and resid 104 through 118 Processing helix chain '1' and resid 161 through 174 Proline residue: 1 167 - end of helix Processing helix chain '1' and resid 195 through 214 Processing helix chain '2' and resid 90 through 108 removed outlier: 3.654A pdb=" N ALA 2 108 " --> pdb=" O VAL 2 104 " (cutoff:3.500A) Processing helix chain '2' and resid 121 through 139 Processing helix chain '2' and resid 178 through 182 Processing helix chain '2' and resid 183 through 192 removed outlier: 4.182A pdb=" N LEU 2 187 " --> pdb=" O MET 2 183 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL 2 191 " --> pdb=" O LEU 2 187 " (cutoff:3.500A) Processing helix chain '2' and resid 194 through 198 Processing helix chain '2' and resid 202 through 221 Processing helix chain '2' and resid 252 through 258 removed outlier: 3.847A pdb=" N LYS 2 256 " --> pdb=" O ASP 2 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 86 through 109 Processing helix chain 'A' and resid 113 through 131 Processing helix chain 'A' and resid 174 through 188 Processing helix chain 'A' and resid 198 through 215 removed outlier: 3.582A pdb=" N VAL A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'B' and resid 18 through 30 removed outlier: 3.827A pdb=" N ASP B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 78 through 96 Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 106 through 123 removed outlier: 3.859A pdb=" N ALA B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 184 through 200 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 239 through 250 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 78 through 100 removed outlier: 3.526A pdb=" N SER C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG C 83 " --> pdb=" O ASN C 79 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 123 removed outlier: 3.812A pdb=" N TYR C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR C 121 " --> pdb=" O GLN C 117 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN C 122 " --> pdb=" O GLN C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 178 removed outlier: 3.663A pdb=" N GLU C 173 " --> pdb=" O LYS C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 201 Processing helix chain 'C' and resid 225 through 243 removed outlier: 3.690A pdb=" N GLN C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 28 Processing helix chain 'D' and resid 78 through 100 removed outlier: 4.526A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 removed outlier: 3.956A pdb=" N TYR D 120 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 177 removed outlier: 3.576A pdb=" N LYS D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 200 Processing helix chain 'D' and resid 205 through 208 removed outlier: 3.609A pdb=" N LYS D 208 " --> pdb=" O THR D 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 205 through 208' Processing helix chain 'D' and resid 225 through 241 removed outlier: 3.665A pdb=" N TYR D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU D 239 " --> pdb=" O GLN D 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 82 through 104 Processing helix chain 'E' and resid 108 through 118 Processing helix chain 'E' and resid 175 through 187 removed outlier: 4.718A pdb=" N ALA E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU E 182 " --> pdb=" O GLY E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 207 Processing helix chain 'E' and resid 232 through 248 Processing helix chain 'F' and resid 19 through 32 removed outlier: 3.933A pdb=" N ALA F 25 " --> pdb=" O GLN F 21 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 100 Processing helix chain 'F' and resid 104 through 120 removed outlier: 4.013A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR F 120 " --> pdb=" O ALA F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 180 removed outlier: 4.414A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ASP F 177 " --> pdb=" O GLU F 173 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N THR F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 198 Processing helix chain 'F' and resid 227 through 232 removed outlier: 4.130A pdb=" N LYS F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 80 through 102 Processing helix chain 'G' and resid 107 through 122 Processing helix chain 'G' and resid 167 through 182 Processing helix chain 'G' and resid 187 through 205 removed outlier: 3.616A pdb=" N LYS G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP G 205 " --> pdb=" O LEU G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 247 Processing helix chain 'H' and resid 67 through 90 Processing helix chain 'H' and resid 93 through 108 Processing helix chain 'H' and resid 147 through 152 removed outlier: 3.895A pdb=" N THR H 151 " --> pdb=" O SER H 148 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE H 152 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 161 Processing helix chain 'H' and resid 166 through 185 Processing helix chain 'H' and resid 208 through 213 Processing helix chain 'I' and resid 78 through 100 Processing helix chain 'I' and resid 104 through 119 removed outlier: 3.680A pdb=" N TYR I 119 " --> pdb=" O HIS I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 removed outlier: 3.546A pdb=" N VAL I 166 " --> pdb=" O ALA I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 195 Processing helix chain 'J' and resid 4 through 8 removed outlier: 4.710A pdb=" N ASN J 8 " --> pdb=" O PRO J 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 4 through 8' Processing helix chain 'J' and resid 56 through 79 Processing helix chain 'J' and resid 83 through 97 Processing helix chain 'J' and resid 142 through 154 Processing helix chain 'J' and resid 159 through 176 Processing helix chain 'K' and resid 49 through 72 removed outlier: 3.970A pdb=" N VAL K 54 " --> pdb=" O ALA K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 93 removed outlier: 4.375A pdb=" N ARG K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 148 removed outlier: 3.860A pdb=" N TYR K 139 " --> pdb=" O TYR K 135 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR K 140 " --> pdb=" O SER K 136 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N SER K 142 " --> pdb=" O PHE K 138 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU K 143 " --> pdb=" O TYR K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 172 Processing helix chain 'L' and resid 123 through 146 Processing helix chain 'L' and resid 150 through 165 Processing helix chain 'L' and resid 207 through 219 removed outlier: 3.795A pdb=" N SER L 217 " --> pdb=" O GLY L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 243 Processing helix chain 'L' and resid 268 through 280 removed outlier: 4.795A pdb=" N TRP L 273 " --> pdb=" O GLY L 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 98 Processing helix chain 'M' and resid 104 through 118 Processing helix chain 'M' and resid 161 through 174 Proline residue: M 167 - end of helix Processing helix chain 'M' and resid 195 through 214 Processing helix chain 'N' and resid 90 through 108 Processing helix chain 'N' and resid 121 through 139 Processing helix chain 'N' and resid 178 through 182 Processing helix chain 'N' and resid 183 through 192 removed outlier: 4.327A pdb=" N LEU N 187 " --> pdb=" O MET N 183 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL N 191 " --> pdb=" O LEU N 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 194 through 198 Processing helix chain 'N' and resid 202 through 221 Processing helix chain 'N' and resid 252 through 258 removed outlier: 3.822A pdb=" N LYS N 256 " --> pdb=" O ASP N 253 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 34 Processing helix chain 'O' and resid 35 through 37 No H-bonds generated for 'chain 'O' and resid 35 through 37' Processing helix chain 'O' and resid 65 through 69 Processing helix chain 'O' and resid 86 through 109 Processing helix chain 'O' and resid 113 through 131 Processing helix chain 'O' and resid 174 through 188 removed outlier: 3.553A pdb=" N ILE O 178 " --> pdb=" O LYS O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 198 through 215 Processing helix chain 'O' and resid 237 through 250 Processing helix chain 'P' and resid 20 through 30 Processing helix chain 'P' and resid 57 through 61 Processing helix chain 'P' and resid 78 through 96 Processing helix chain 'P' and resid 97 through 102 Processing helix chain 'P' and resid 106 through 123 removed outlier: 3.831A pdb=" N ALA P 121 " --> pdb=" O ILE P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 179 removed outlier: 3.574A pdb=" N LYS P 177 " --> pdb=" O THR P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 200 Processing helix chain 'P' and resid 218 through 222 Processing helix chain 'P' and resid 239 through 250 Processing helix chain 'Q' and resid 12 through 16 removed outlier: 4.260A pdb=" N HIS Q 16 " --> pdb=" O PRO Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 29 Processing helix chain 'Q' and resid 78 through 100 removed outlier: 3.659A pdb=" N ARG Q 83 " --> pdb=" O ASN Q 79 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE Q 84 " --> pdb=" O ALA Q 80 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG Q 97 " --> pdb=" O ALA Q 93 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 123 removed outlier: 3.731A pdb=" N TYR Q 120 " --> pdb=" O VAL Q 116 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR Q 121 " --> pdb=" O GLN Q 117 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN Q 122 " --> pdb=" O GLN Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 178 removed outlier: 4.814A pdb=" N GLU Q 173 " --> pdb=" O LYS Q 169 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 202 Processing helix chain 'Q' and resid 225 through 243 Processing helix chain 'R' and resid 19 through 28 Processing helix chain 'R' and resid 78 through 100 removed outlier: 4.486A pdb=" N ILE R 84 " --> pdb=" O ALA R 80 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU R 85 " --> pdb=" O ASP R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 120 removed outlier: 3.755A pdb=" N TYR R 120 " --> pdb=" O VAL R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 177 removed outlier: 3.511A pdb=" N LYS R 177 " --> pdb=" O GLU R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 200 Processing helix chain 'R' and resid 205 through 209 Processing helix chain 'R' and resid 225 through 241 removed outlier: 3.861A pdb=" N GLU R 239 " --> pdb=" O GLN R 235 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 64 Processing helix chain 'S' and resid 82 through 104 Processing helix chain 'S' and resid 108 through 118 Processing helix chain 'S' and resid 175 through 187 removed outlier: 4.709A pdb=" N ALA S 181 " --> pdb=" O GLU S 177 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU S 182 " --> pdb=" O GLY S 178 " (cutoff:3.500A) Processing helix chain 'S' and resid 192 through 208 removed outlier: 3.515A pdb=" N LEU S 198 " --> pdb=" O LYS S 194 " (cutoff:3.500A) Processing helix chain 'S' and resid 232 through 248 Processing helix chain 'T' and resid 19 through 32 removed outlier: 3.645A pdb=" N ALA T 25 " --> pdb=" O GLN T 21 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY T 32 " --> pdb=" O ALA T 28 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 100 Processing helix chain 'T' and resid 104 through 120 removed outlier: 3.526A pdb=" N LYS T 118 " --> pdb=" O ASP T 114 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN T 119 " --> pdb=" O LYS T 115 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR T 120 " --> pdb=" O ALA T 116 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 180 removed outlier: 4.366A pdb=" N ALA T 168 " --> pdb=" O ARG T 164 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASP T 177 " --> pdb=" O GLU T 173 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N THR T 178 " --> pdb=" O ARG T 174 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE T 180 " --> pdb=" O LEU T 176 " (cutoff:3.500A) Processing helix chain 'T' and resid 186 through 198 Processing helix chain 'T' and resid 199 through 201 No H-bonds generated for 'chain 'T' and resid 199 through 201' Processing helix chain 'T' and resid 228 through 233 removed outlier: 3.964A pdb=" N LYS T 232 " --> pdb=" O ALA T 229 " (cutoff:3.500A) Processing helix chain 'U' and resid 20 through 31 Processing helix chain 'U' and resid 80 through 102 Processing helix chain 'U' and resid 107 through 122 Processing helix chain 'U' and resid 167 through 182 Processing helix chain 'U' and resid 187 through 204 removed outlier: 3.803A pdb=" N LYS U 193 " --> pdb=" O ARG U 189 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU U 204 " --> pdb=" O TYR U 200 " (cutoff:3.500A) Processing helix chain 'U' and resid 205 through 207 No H-bonds generated for 'chain 'U' and resid 205 through 207' Processing helix chain 'U' and resid 231 through 247 Processing helix chain 'V' and resid 67 through 90 Processing helix chain 'V' and resid 93 through 108 Processing helix chain 'V' and resid 149 through 152 Processing helix chain 'V' and resid 153 through 161 Processing helix chain 'V' and resid 166 through 185 Processing helix chain 'V' and resid 208 through 213 Processing helix chain 'W' and resid 78 through 100 Processing helix chain 'W' and resid 104 through 119 removed outlier: 3.659A pdb=" N TYR W 119 " --> pdb=" O HIS W 115 " (cutoff:3.500A) Processing helix chain 'W' and resid 159 through 171 Processing helix chain 'W' and resid 176 through 195 Processing helix chain 'X' and resid 4 through 8 removed outlier: 4.597A pdb=" N ASN X 8 " --> pdb=" O PRO X 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 4 through 8' Processing helix chain 'X' and resid 56 through 79 Processing helix chain 'X' and resid 83 through 97 Processing helix chain 'X' and resid 142 through 154 Processing helix chain 'X' and resid 159 through 176 Processing helix chain 'Y' and resid 49 through 72 removed outlier: 3.949A pdb=" N VAL Y 54 " --> pdb=" O ALA Y 50 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 93 removed outlier: 4.419A pdb=" N ARG Y 93 " --> pdb=" O ALA Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 148 removed outlier: 3.919A pdb=" N TYR Y 139 " --> pdb=" O TYR Y 135 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N SER Y 142 " --> pdb=" O PHE Y 138 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU Y 143 " --> pdb=" O TYR Y 139 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 172 Processing helix chain 'Z' and resid 123 through 146 Processing helix chain 'Z' and resid 150 through 165 Processing helix chain 'Z' and resid 207 through 219 removed outlier: 3.570A pdb=" N VAL Z 214 " --> pdb=" O PHE Z 210 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER Z 217 " --> pdb=" O GLY Z 213 " (cutoff:3.500A) Processing helix chain 'Z' and resid 224 through 243 Processing helix chain 'Z' and resid 268 through 280 removed outlier: 4.826A pdb=" N TRP Z 273 " --> pdb=" O GLY Z 269 " (cutoff:3.500A) Processing helix chain 'a' and resid 152 through 155 Processing helix chain 'a' and resid 156 through 161 Processing helix chain 'a' and resid 167 through 172 Processing helix chain 'a' and resid 209 through 213 Processing helix chain 'b' and resid 152 through 155 Processing helix chain 'b' and resid 156 through 161 Processing helix chain 'b' and resid 167 through 172 Processing sheet with id=AA1, first strand: chain '1' and resid 155 through 159 removed outlier: 5.295A pdb=" N THR 1 30 " --> pdb=" O ASP 1 45 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE 1 39 " --> pdb=" O GLY 1 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 48 through 50 removed outlier: 6.846A pdb=" N ASN 1 48 " --> pdb=" O ASN 1 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 62 through 64 removed outlier: 3.695A pdb=" N ASN 1 74 " --> pdb=" O HIS 1 127 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR 1 128 " --> pdb=" O PHE 1 144 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL 1 141 " --> pdb=" O GLU 1 153 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP 1 145 " --> pdb=" O SER 1 149 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N SER 1 149 " --> pdb=" O ASP 1 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 66 through 69 removed outlier: 5.341A pdb=" N LEU 2 67 " --> pdb=" O TYR 2 63 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR 2 63 " --> pdb=" O LEU 2 67 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR 2 82 " --> pdb=" O VAL 2 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 66 through 69 removed outlier: 5.341A pdb=" N LEU 2 67 " --> pdb=" O TYR 2 63 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR 2 63 " --> pdb=" O LEU 2 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 174 through 176 removed outlier: 5.699A pdb=" N PHE 2 228 " --> pdb=" O ASN 2 244 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN 2 244 " --> pdb=" O PHE 2 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 168 through 171 Processing sheet with id=AA8, first strand: chain 'A' and resid 72 through 74 Processing sheet with id=AA9, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.711A pdb=" N GLY B 42 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU B 211 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 65 through 68 removed outlier: 5.612A pdb=" N LEU B 66 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA B 73 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 224 through 225 removed outlier: 6.303A pdb=" N THR B 225 " --> pdb=" O TYR I 215 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG I 217 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ASP I 212 " --> pdb=" O GLU I 208 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLU I 208 " --> pdb=" O ASP I 212 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN I 218 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL I 202 " --> pdb=" O ASN I 218 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 161 through 164 Processing sheet with id=AB4, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.685A pdb=" N VAL C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY C 137 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS C 146 " --> pdb=" O GLY C 137 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 161 through 164 Processing sheet with id=AB6, first strand: chain 'D' and resid 65 through 68 removed outlier: 6.614A pdb=" N VAL D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 169 through 172 Processing sheet with id=AB8, first strand: chain 'E' and resid 67 through 71 removed outlier: 5.972A pdb=" N ILE E 67 " --> pdb=" O MET E 78 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N MET E 78 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLU E 69 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N CYS E 76 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU E 142 " --> pdb=" O ALA E 158 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA E 158 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 158 through 161 removed outlier: 5.792A pdb=" N GLY F 217 " --> pdb=" O PRO F 221 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 63 through 67 removed outlier: 6.255A pdb=" N MET F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 161 through 164 removed outlier: 3.623A pdb=" N GLY G 44 " --> pdb=" O CYS G 41 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 67 through 69 Processing sheet with id=AC4, first strand: chain 'H' and resid 143 through 146 Processing sheet with id=AC5, first strand: chain 'H' and resid 39 through 41 removed outlier: 7.027A pdb=" N THR H 39 " --> pdb=" O ALA H 46 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 53 through 57 removed outlier: 6.481A pdb=" N ILE H 60 " --> pdb=" O VAL H 56 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 49 through 51 removed outlier: 6.377A pdb=" N GLN I 51 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL I 55 " --> pdb=" O GLN I 51 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 64 through 67 removed outlier: 6.161A pdb=" N ILE I 70 " --> pdb=" O ILE I 66 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 64 through 67 removed outlier: 6.161A pdb=" N ILE I 70 " --> pdb=" O ILE I 66 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 241 through 246 removed outlier: 6.554A pdb=" N TYR J 199 " --> pdb=" O LEU I 242 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU I 244 " --> pdb=" O LYS J 197 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS J 197 " --> pdb=" O GLU I 244 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE I 246 " --> pdb=" O VAL J 195 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL J 195 " --> pdb=" O ILE I 246 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA J 185 " --> pdb=" O LEU J 200 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE J 11 " --> pdb=" O ASP J 26 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 29 through 31 removed outlier: 6.611A pdb=" N LEU J 29 " --> pdb=" O VAL J 36 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 43 through 46 removed outlier: 3.674A pdb=" N VAL J 49 " --> pdb=" O TYR J 46 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 130 through 132 removed outlier: 4.643A pdb=" N VAL K 181 " --> pdb=" O VAL K 192 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 21 through 23 removed outlier: 6.630A pdb=" N ARG K 23 " --> pdb=" O VAL K 27 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL K 27 " --> pdb=" O ARG K 23 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 35 through 39 removed outlier: 6.408A pdb=" N THR K 42 " --> pdb=" O LEU K 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 201 through 204 removed outlier: 3.989A pdb=" N GLY L 264 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N HIS L 254 " --> pdb=" O TYR L 262 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N TYR L 262 " --> pdb=" O HIS L 254 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N THR L 256 " --> pdb=" O TRP L 260 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N TRP L 260 " --> pdb=" O THR L 256 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 95 through 97 removed outlier: 6.856A pdb=" N ALA L 95 " --> pdb=" O ALA L 102 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 109 through 113 removed outlier: 6.411A pdb=" N LEU L 116 " --> pdb=" O ILE L 112 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 155 through 159 removed outlier: 5.327A pdb=" N THR M 30 " --> pdb=" O ASP M 45 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 48 through 50 removed outlier: 6.734A pdb=" N ASN M 48 " --> pdb=" O ASN M 55 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 63 through 64 removed outlier: 3.617A pdb=" N ASN M 74 " --> pdb=" O HIS M 127 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL M 141 " --> pdb=" O GLU M 153 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 66 through 69 removed outlier: 5.382A pdb=" N LEU N 67 " --> pdb=" O TYR N 63 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR N 63 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N THR N 82 " --> pdb=" O VAL N 78 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 66 through 69 removed outlier: 5.382A pdb=" N LEU N 67 " --> pdb=" O TYR N 63 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR N 63 " --> pdb=" O LEU N 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 174 through 176 removed outlier: 5.738A pdb=" N PHE N 228 " --> pdb=" O ASN N 244 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN N 244 " --> pdb=" O PHE N 228 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 168 through 171 Processing sheet with id=AE8, first strand: chain 'O' and resid 72 through 74 Processing sheet with id=AE9, first strand: chain 'P' and resid 161 through 164 removed outlier: 3.575A pdb=" N GLY P 42 " --> pdb=" O ALA P 39 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU P 211 " --> pdb=" O LEU P 238 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 65 through 68 removed outlier: 6.479A pdb=" N ILE P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 224 through 225 removed outlier: 6.250A pdb=" N THR P 225 " --> pdb=" O TYR W 215 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ARG W 217 " --> pdb=" O THR P 225 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASP W 212 " --> pdb=" O GLU W 208 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU W 208 " --> pdb=" O ASP W 212 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN W 218 " --> pdb=" O VAL W 202 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL W 202 " --> pdb=" O ASN W 218 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 161 through 164 Processing sheet with id=AF4, first strand: chain 'Q' and resid 65 through 66 removed outlier: 3.562A pdb=" N GLY Q 137 " --> pdb=" O LYS Q 146 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU Q 151 " --> pdb=" O ILE Q 155 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE Q 155 " --> pdb=" O GLU Q 151 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 161 through 164 removed outlier: 3.504A pdb=" N GLN R 162 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL R 42 " --> pdb=" O VAL R 215 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'R' and resid 65 through 68 removed outlier: 6.729A pdb=" N VAL R 71 " --> pdb=" O ILE R 67 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 169 through 172 Processing sheet with id=AF8, first strand: chain 'S' and resid 67 through 71 removed outlier: 5.820A pdb=" N ILE S 67 " --> pdb=" O MET S 78 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N MET S 78 " --> pdb=" O ILE S 67 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLU S 69 " --> pdb=" O CYS S 76 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N CYS S 76 " --> pdb=" O GLU S 69 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU S 142 " --> pdb=" O ALA S 158 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA S 158 " --> pdb=" O LEU S 142 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU S 155 " --> pdb=" O TYR S 167 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'T' and resid 158 through 161 Processing sheet with id=AG1, first strand: chain 'T' and resid 63 through 67 removed outlier: 6.659A pdb=" N MET T 70 " --> pdb=" O CYS T 66 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 161 through 164 Processing sheet with id=AG3, first strand: chain 'U' and resid 67 through 69 Processing sheet with id=AG4, first strand: chain 'V' and resid 143 through 146 Processing sheet with id=AG5, first strand: chain 'V' and resid 39 through 41 removed outlier: 6.462A pdb=" N THR V 41 " --> pdb=" O ILE V 45 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ILE V 45 " --> pdb=" O THR V 41 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'V' and resid 53 through 57 removed outlier: 6.625A pdb=" N ILE V 60 " --> pdb=" O VAL V 56 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE V 117 " --> pdb=" O CYS V 63 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'W' and resid 49 through 51 removed outlier: 6.271A pdb=" N GLN W 51 " --> pdb=" O VAL W 55 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N VAL W 55 " --> pdb=" O GLN W 51 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'W' and resid 64 through 67 removed outlier: 6.178A pdb=" N ILE W 70 " --> pdb=" O ILE W 66 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'W' and resid 64 through 67 removed outlier: 6.178A pdb=" N ILE W 70 " --> pdb=" O ILE W 66 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'W' and resid 241 through 246 removed outlier: 6.533A pdb=" N TYR X 199 " --> pdb=" O LEU W 242 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU W 244 " --> pdb=" O LYS X 197 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS X 197 " --> pdb=" O GLU W 244 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE W 246 " --> pdb=" O VAL X 195 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL X 195 " --> pdb=" O ILE W 246 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA X 185 " --> pdb=" O LEU X 200 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ILE X 11 " --> pdb=" O ASP X 26 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'X' and resid 29 through 31 removed outlier: 6.572A pdb=" N LEU X 29 " --> pdb=" O VAL X 36 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'X' and resid 43 through 46 removed outlier: 3.661A pdb=" N VAL X 49 " --> pdb=" O TYR X 46 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Y' and resid 130 through 132 removed outlier: 4.782A pdb=" N VAL Y 181 " --> pdb=" O VAL Y 192 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Y' and resid 21 through 23 removed outlier: 6.768A pdb=" N VAL Y 21 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Y' and resid 35 through 39 removed outlier: 6.410A pdb=" N THR Y 42 " --> pdb=" O LEU Y 38 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Z' and resid 201 through 204 removed outlier: 3.896A pdb=" N GLY Z 264 " --> pdb=" O LEU Z 252 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS Z 254 " --> pdb=" O TYR Z 262 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N TYR Z 262 " --> pdb=" O HIS Z 254 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR Z 256 " --> pdb=" O TRP Z 260 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N TRP Z 260 " --> pdb=" O THR Z 256 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Z' and resid 95 through 97 removed outlier: 6.296A pdb=" N ALA Z 97 " --> pdb=" O VAL Z 101 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL Z 101 " --> pdb=" O ALA Z 97 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Z' and resid 109 through 113 removed outlier: 6.381A pdb=" N LEU Z 116 " --> pdb=" O ILE Z 112 " (cutoff:3.500A) 2822 hydrogen bonds defined for protein. 7989 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 43.01 Time building geometry restraints manager: 78.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 48536 1.04 - 1.24: 5728 1.24 - 1.44: 15509 1.44 - 1.64: 28399 1.64 - 1.84: 248 Bond restraints: 98420 Sorted by residual: bond pdb=" N PHE 1 21 " pdb=" CA PHE 1 21 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.24e+00 bond pdb=" N HIS O 15 " pdb=" CA HIS O 15 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.20e+00 bond pdb=" N THR P 10 " pdb=" CA THR P 10 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 bond pdb=" N PHE D 18 " pdb=" CA PHE D 18 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N PHE R 18 " pdb=" CA PHE R 18 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 ... (remaining 98415 not shown) Histogram of bond angle deviations from ideal: 99.86 - 106.73: 1299 106.73 - 113.59: 117806 113.59 - 120.46: 31953 120.46 - 127.33: 26352 127.33 - 134.19: 434 Bond angle restraints: 177844 Sorted by residual: angle pdb=" C GLN J 32 " pdb=" CA GLN J 32 " pdb=" CB GLN J 32 " ideal model delta sigma weight residual 117.23 111.58 5.65 1.36e+00 5.41e-01 1.72e+01 angle pdb=" N GLU L 142 " pdb=" CA GLU L 142 " pdb=" CB GLU L 142 " ideal model delta sigma weight residual 110.12 115.88 -5.76 1.47e+00 4.63e-01 1.53e+01 angle pdb=" N GLY 1 218 " pdb=" CA GLY 1 218 " pdb=" C GLY 1 218 " ideal model delta sigma weight residual 113.18 122.33 -9.15 2.37e+00 1.78e-01 1.49e+01 angle pdb=" N GLY M 218 " pdb=" CA GLY M 218 " pdb=" C GLY M 218 " ideal model delta sigma weight residual 113.18 121.95 -8.77 2.37e+00 1.78e-01 1.37e+01 angle pdb=" N VAL D 202 " pdb=" CA VAL D 202 " pdb=" C VAL D 202 " ideal model delta sigma weight residual 113.71 110.30 3.41 9.50e-01 1.11e+00 1.29e+01 ... (remaining 177839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 36288 17.97 - 35.93: 2046 35.93 - 53.90: 562 53.90 - 71.87: 263 71.87 - 89.84: 109 Dihedral angle restraints: 39268 sinusoidal: 18276 harmonic: 20992 Sorted by residual: dihedral pdb=" CA VAL 1 217 " pdb=" C VAL 1 217 " pdb=" N GLY 1 218 " pdb=" CA GLY 1 218 " ideal model delta harmonic sigma weight residual -180.00 -151.18 -28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA VAL M 217 " pdb=" C VAL M 217 " pdb=" N GLY M 218 " pdb=" CA GLY M 218 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ILE M 165 " pdb=" C ILE M 165 " pdb=" N MET M 166 " pdb=" CA MET M 166 " ideal model delta harmonic sigma weight residual 180.00 -156.41 -23.59 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 39265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 4745 0.030 - 0.061: 1811 0.061 - 0.091: 495 0.091 - 0.121: 437 0.121 - 0.152: 96 Chirality restraints: 7584 Sorted by residual: chirality pdb=" CA VAL N 44 " pdb=" N VAL N 44 " pdb=" C VAL N 44 " pdb=" CB VAL N 44 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE G 136 " pdb=" N ILE G 136 " pdb=" C ILE G 136 " pdb=" CB ILE G 136 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA ILE U 136 " pdb=" N ILE U 136 " pdb=" C ILE U 136 " pdb=" CB ILE U 136 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 7581 not shown) Planarity restraints: 14712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP Q 139 " 0.055 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO Q 140 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO Q 140 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO Q 140 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER P 13 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO P 14 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO P 14 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO P 14 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY X 106 " 0.047 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO X 107 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO X 107 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO X 107 " 0.039 5.00e-02 4.00e+02 ... (remaining 14709 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 2071 2.11 - 2.73: 175068 2.73 - 3.35: 290349 3.35 - 3.98: 380488 3.98 - 4.60: 601850 Nonbonded interactions: 1449826 Sorted by model distance: nonbonded pdb=" O GLY 1 218 " pdb=" H ARG 1 240 " model vdw 1.484 1.850 nonbonded pdb=" O GLY M 218 " pdb=" H ARG M 240 " model vdw 1.524 1.850 nonbonded pdb=" HH TYR K 139 " pdb=" O ILE Y 25 " model vdw 1.539 1.850 nonbonded pdb=" OD1 ASP N 58 " pdb="HH21 ARG N 74 " model vdw 1.540 1.850 nonbonded pdb=" OD1 ASP 2 58 " pdb="HH21 ARG 2 74 " model vdw 1.542 1.850 ... (remaining 1449821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '1' selection = chain 'M' } ncs_group { reference = chain '2' selection = chain 'N' } ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = (chain 'C' and (resid 18 through 48 or resid 62 through 121 or resid 127 through \ 243)) selection = (chain 'D' and (resid 18 through 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name H \ E2)) or resid 71 through 178 or resid 183 through 203 or resid 208 through 243)) \ selection = (chain 'Q' and (resid 18 through 48 or resid 62 through 121 or resid 127 through \ 243)) selection = (chain 'R' and (resid 18 through 178 or resid 183 through 203 or resid 208 throu \ gh 243)) } ncs_group { reference = (chain 'E' and (resid 13 through 98 or (resid 99 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name H \ E1)) or resid 100 through 248)) selection = (chain 'S' and (resid 13 through 187 or (resid 188 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 189 through 248)) } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = (chain 'H' and (resid 20 through 56 or (resid 57 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name H \ E1)) or resid 58 through 215)) selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'a' selection = chain 'b' } 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 S 162 5.16 5 C 30952 2.51 5 N 8304 2.21 5 O 9492 1.98 5 H 48612 0.53 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.120 Extract box with map and model: 16.240 Check model and map are aligned: 1.160 Convert atoms to be neutral: 0.620 Process input model: 263.120 Find NCS groups from input model: 4.630 Set up NCS constraints: 0.560 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 304.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 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 : 0.003 0.051 49808 Z= 0.185 Angle : 0.548 9.145 67374 Z= 0.311 Chirality : 0.043 0.152 7584 Planarity : 0.004 0.082 8704 Dihedral : 12.701 89.834 18354 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.10), residues: 6180 helix: 1.48 (0.11), residues: 2252 sheet: 0.39 (0.13), residues: 1484 loop : 0.08 (0.13), residues: 2444 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 774 time to evaluate : 6.165 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 revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 774 average time/residue: 2.4265 time to fit residues: 2452.3113 Evaluate side-chains 483 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 482 time to evaluate : 6.036 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 7.4362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 523 optimal weight: 2.9990 chunk 469 optimal weight: 5.9990 chunk 260 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 316 optimal weight: 3.9990 chunk 251 optimal weight: 5.9990 chunk 485 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 295 optimal weight: 4.9990 chunk 361 optimal weight: 4.9990 chunk 563 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN 1 113 GLN 2 244 ASN B 205 ASN E 73 HIS E 108 ASN E 185 ASN G 126 ASN H 214 GLN K 147 HIS L 128 GLN M 113 GLN ** O 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 241 GLN R 94 GLN S 185 ASN U 61 GLN U 126 ASN U 247 ASN Y 65 GLN Z 128 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 49808 Z= 0.423 Angle : 0.614 9.523 67374 Z= 0.339 Chirality : 0.047 0.181 7584 Planarity : 0.005 0.083 8704 Dihedral : 5.383 51.308 6808 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.10), residues: 6180 helix: 1.44 (0.10), residues: 2282 sheet: 0.22 (0.13), residues: 1494 loop : -0.27 (0.12), residues: 2404 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 484 time to evaluate : 6.239 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 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: 100 outliers final: 43 residues processed: 552 average time/residue: 2.4511 time to fit residues: 1795.5291 Evaluate side-chains 492 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 449 time to evaluate : 6.145 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 26 residues processed: 17 average time/residue: 1.2201 time to fit residues: 41.1503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 312 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 468 optimal weight: 2.9990 chunk 383 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 564 optimal weight: 2.9990 chunk 609 optimal weight: 10.0000 chunk 502 optimal weight: 0.9980 chunk 559 optimal weight: 0.0270 chunk 192 optimal weight: 4.9990 chunk 452 optimal weight: 9.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN B 205 ASN E 185 ASN K 99 GLN O 209 HIS S 185 ASN U 243 GLN Y 99 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 49808 Z= 0.225 Angle : 0.524 8.206 67374 Z= 0.285 Chirality : 0.043 0.164 7584 Planarity : 0.004 0.081 8704 Dihedral : 5.098 42.411 6808 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.10), residues: 6180 helix: 1.71 (0.11), residues: 2288 sheet: 0.19 (0.13), residues: 1490 loop : -0.32 (0.12), residues: 2402 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 507 time to evaluate : 6.108 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 44 residues processed: 557 average time/residue: 2.3497 time to fit residues: 1734.8038 Evaluate side-chains 487 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 443 time to evaluate : 6.060 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 28 residues processed: 16 average time/residue: 1.5367 time to fit residues: 44.2079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 557 optimal weight: 3.9990 chunk 424 optimal weight: 7.9990 chunk 292 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 269 optimal weight: 1.9990 chunk 378 optimal weight: 3.9990 chunk 566 optimal weight: 3.9990 chunk 599 optimal weight: 3.9990 chunk 295 optimal weight: 4.9990 chunk 536 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN B 205 ASN E 185 ASN K 99 GLN O 209 HIS S 185 ASN U 243 GLN Y 99 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 49808 Z= 0.406 Angle : 0.571 7.512 67374 Z= 0.313 Chirality : 0.045 0.167 7584 Planarity : 0.004 0.081 8704 Dihedral : 5.149 33.983 6808 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.10), residues: 6180 helix: 1.65 (0.10), residues: 2292 sheet: -0.02 (0.13), residues: 1460 loop : -0.54 (0.12), residues: 2428 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 451 time to evaluate : 6.644 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 53 residues processed: 529 average time/residue: 2.4039 time to fit residues: 1685.9840 Evaluate side-chains 496 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 443 time to evaluate : 6.098 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 35 residues processed: 18 average time/residue: 1.2784 time to fit residues: 44.3063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 499 optimal weight: 2.9990 chunk 340 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 446 optimal weight: 7.9990 chunk 247 optimal weight: 1.9990 chunk 511 optimal weight: 4.9990 chunk 414 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 306 optimal weight: 4.9990 chunk 537 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN B 205 ASN E 185 ASN K 99 GLN S 185 ASN U 243 GLN V 164 ASN Y 99 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 49808 Z= 0.274 Angle : 0.525 6.398 67374 Z= 0.285 Chirality : 0.044 0.164 7584 Planarity : 0.004 0.079 8704 Dihedral : 5.001 29.891 6808 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.10), residues: 6180 helix: 1.85 (0.11), residues: 2282 sheet: -0.04 (0.13), residues: 1462 loop : -0.51 (0.12), residues: 2436 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 478 time to evaluate : 6.148 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 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: 87 outliers final: 51 residues processed: 538 average time/residue: 2.3416 time to fit residues: 1679.9876 Evaluate side-chains 493 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 442 time to evaluate : 6.128 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 38 residues processed: 13 average time/residue: 1.2741 time to fit residues: 34.1343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 201 optimal weight: 3.9990 chunk 539 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 351 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 599 optimal weight: 3.9990 chunk 497 optimal weight: 6.9990 chunk 277 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 198 optimal weight: 8.9990 chunk 314 optimal weight: 0.0570 overall best weight: 1.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN B 205 ASN E 185 ASN O 209 HIS S 108 ASN S 185 ASN U 243 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 49808 Z= 0.228 Angle : 0.504 6.460 67374 Z= 0.272 Chirality : 0.043 0.163 7584 Planarity : 0.004 0.078 8704 Dihedral : 4.839 28.130 6808 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.10), residues: 6180 helix: 2.03 (0.11), residues: 2276 sheet: -0.04 (0.13), residues: 1488 loop : -0.42 (0.12), residues: 2416 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 464 time to evaluate : 6.294 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 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: 98 outliers final: 57 residues processed: 533 average time/residue: 2.2884 time to fit residues: 1641.7140 Evaluate side-chains 495 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 438 time to evaluate : 6.194 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 41 residues processed: 16 average time/residue: 1.3574 time to fit residues: 42.2155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 578 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 341 optimal weight: 3.9990 chunk 438 optimal weight: 6.9990 chunk 339 optimal weight: 0.7980 chunk 504 optimal weight: 4.9990 chunk 334 optimal weight: 3.9990 chunk 597 optimal weight: 2.9990 chunk 373 optimal weight: 3.9990 chunk 364 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN B 205 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN I 194 ASN K 99 GLN S 185 ASN U 243 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.042 49808 Z= 0.373 Angle : 0.547 6.493 67374 Z= 0.298 Chirality : 0.045 0.189 7584 Planarity : 0.004 0.077 8704 Dihedral : 4.945 30.072 6808 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.62 % Favored : 97.35 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.10), residues: 6180 helix: 1.93 (0.10), residues: 2282 sheet: -0.18 (0.12), residues: 1512 loop : -0.58 (0.12), residues: 2386 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 441 time to evaluate : 6.254 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 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 revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 68 residues processed: 511 average time/residue: 2.3123 time to fit residues: 1591.9348 Evaluate side-chains 493 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 425 time to evaluate : 6.056 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 48 residues processed: 21 average time/residue: 1.1595 time to fit residues: 48.1673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 369 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 356 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 379 optimal weight: 0.3980 chunk 407 optimal weight: 6.9990 chunk 295 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 469 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN 2 51 ASN B 205 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN K 146 HIS S 185 ASN U 243 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 49808 Z= 0.290 Angle : 0.523 6.565 67374 Z= 0.283 Chirality : 0.043 0.167 7584 Planarity : 0.004 0.077 8704 Dihedral : 4.878 30.379 6808 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.51 % Favored : 97.46 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.10), residues: 6180 helix: 2.01 (0.11), residues: 2278 sheet: -0.14 (0.13), residues: 1486 loop : -0.59 (0.12), residues: 2416 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 452 time to evaluate : 6.194 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 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 revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 61 residues processed: 518 average time/residue: 2.4052 time to fit residues: 1678.8427 Evaluate side-chains 489 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 428 time to evaluate : 6.124 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 48 residues processed: 13 average time/residue: 1.4743 time to fit residues: 37.0191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 543 optimal weight: 4.9990 chunk 572 optimal weight: 2.9990 chunk 522 optimal weight: 2.9990 chunk 556 optimal weight: 3.9990 chunk 335 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 chunk 437 optimal weight: 9.9990 chunk 170 optimal weight: 8.9990 chunk 503 optimal weight: 2.9990 chunk 526 optimal weight: 2.9990 chunk 554 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN B 205 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN S 185 ASN U 243 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 49808 Z= 0.308 Angle : 0.528 6.466 67374 Z= 0.286 Chirality : 0.044 0.167 7584 Planarity : 0.004 0.076 8704 Dihedral : 4.865 30.733 6808 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.70 % Favored : 97.27 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.10), residues: 6180 helix: 2.01 (0.10), residues: 2282 sheet: -0.17 (0.13), residues: 1486 loop : -0.61 (0.12), residues: 2412 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 439 time to evaluate : 7.517 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 66 residues processed: 505 average time/residue: 2.2838 time to fit residues: 1551.7545 Evaluate side-chains 491 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 425 time to evaluate : 6.111 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 50 residues processed: 17 average time/residue: 1.3187 time to fit residues: 43.4598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 365 optimal weight: 0.9980 chunk 588 optimal weight: 4.9990 chunk 359 optimal weight: 0.9990 chunk 279 optimal weight: 1.9990 chunk 409 optimal weight: 9.9990 chunk 617 optimal weight: 6.9990 chunk 568 optimal weight: 2.9990 chunk 491 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 379 optimal weight: 0.1980 chunk 301 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN B 205 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN ** F 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 GLN S 185 ASN U 243 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 49808 Z= 0.161 Angle : 0.492 6.712 67374 Z= 0.263 Chirality : 0.042 0.167 7584 Planarity : 0.003 0.076 8704 Dihedral : 4.705 28.237 6808 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.02 % Favored : 97.94 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.11), residues: 6180 helix: 2.21 (0.11), residues: 2280 sheet: -0.14 (0.13), residues: 1516 loop : -0.41 (0.12), residues: 2384 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 456 time to evaluate : 6.227 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 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 revert: symmetry clash outliers start: 62 outliers final: 48 residues processed: 510 average time/residue: 2.3340 time to fit residues: 1585.7322 Evaluate side-chains 480 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 432 time to evaluate : 6.183 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 44 residues processed: 4 average time/residue: 1.1666 time to fit residues: 14.9703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 390 optimal weight: 0.8980 chunk 523 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 453 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 chunk 492 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 505 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN G 243 GLN M 99 ASN S 185 ASN U 243 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.132449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.102842 restraints weight = 201202.017| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.83 r_work: 0.3158 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 49808 Z= 0.212 Angle : 0.498 6.902 67374 Z= 0.267 Chirality : 0.042 0.186 7584 Planarity : 0.004 0.077 8704 Dihedral : 4.661 26.828 6808 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.36 % Favored : 97.62 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.11), residues: 6180 helix: 2.26 (0.11), residues: 2276 sheet: -0.12 (0.13), residues: 1504 loop : -0.43 (0.12), residues: 2400 =============================================================================== Job complete usr+sys time: 25700.07 seconds wall clock time: 443 minutes 57.09 seconds (26637.09 seconds total)