Starting phenix.real_space_refine (version: dev) on Thu Dec 22 19:10:10 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3k_25661/12_2022/7t3k_25661.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3k_25661/12_2022/7t3k_25661.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3k_25661/12_2022/7t3k_25661.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3k_25661/12_2022/7t3k_25661.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3k_25661/12_2022/7t3k_25661.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3k_25661/12_2022/7t3k_25661.pdb" } resolution = 3.5 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= 0.010 sd= 0.055 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 "D GLU 34": "OE1" <-> "OE2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "G GLU 302": "OE1" <-> "OE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H GLU 188": "OE1" <-> "OE2" Residue "H TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "I TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "K PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 134": "OE1" <-> "OE2" Residue "K GLU 173": "OE1" <-> "OE2" Residue "d GLU 34": "OE1" <-> "OE2" Residue "d PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 57": "OE1" <-> "OE2" Residue "g GLU 302": "OE1" <-> "OE2" Residue "h GLU 57": "OE1" <-> "OE2" Residue "h GLU 188": "OE1" <-> "OE2" Residue "h TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i GLU 57": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 50620 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3145 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 24, 'TRANS': 402} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 196 Chain: "B" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2411 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 24, 'TRANS': 281} Chain breaks: 1 Chain: "C" Number of atoms: 1448 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1480 Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2307 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Chain: "E" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "F" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "G" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "H" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "I" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "J" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 16, 'TRANS': 211} Chain: "K" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 16, 'TRANS': 211} Chain: "M" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1273 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "a" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3145 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 24, 'TRANS': 402} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 196 Chain: "b" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2411 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 24, 'TRANS': 281} Chain breaks: 1 Chain: "c" Number of atoms: 1448 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1480 Chain: "d" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2307 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Chain: "e" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "f" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "g" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "h" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "i" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "m" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1273 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 29.58, per 1000 atoms: 0.58 Number of scatterers: 50620 At special positions: 0 Unit cell: (157.5, 161.7, 236.25, 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 58 16.00 P 120 15.00 O 9806 8.00 N 9208 7.00 C 31428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.99 Conformation dependent library (CDL) restraints added in 7.8 seconds 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11608 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 103 sheets defined 34.6% alpha, 20.6% beta 10 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 13.82 Creating SS restraints... Processing helix chain 'A' and resid 9 through 33 removed outlier: 3.944A pdb=" N LEU A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 49 through 58 removed outlier: 4.128A pdb=" N LEU A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 115 through 121 removed outlier: 3.899A pdb=" N LYS A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 135 Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 195 through 212 Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 294 through 309 removed outlier: 3.910A pdb=" N ALA A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 340 removed outlier: 3.506A pdb=" N ILE A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.519A pdb=" N ASP A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.774A pdb=" N LEU A 379 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 397 Processing helix chain 'A' and resid 402 through 408 removed outlier: 3.686A pdb=" N LEU A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.728A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.744A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 removed outlier: 3.536A pdb=" N LEU B 118 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 180 Processing helix chain 'B' and resid 189 through 204 Processing helix chain 'B' and resid 208 through 216 Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.902A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.597A pdb=" N LEU B 302 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.899A pdb=" N GLY B 312 " --> pdb=" O PRO B 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 36 removed outlier: 3.991A pdb=" N LEU C 20 " --> pdb=" O PRO C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 Processing helix chain 'C' and resid 74 through 77 removed outlier: 3.528A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 74 through 77' Processing helix chain 'C' and resid 108 through 121 removed outlier: 3.730A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 118 " --> pdb=" O ARG C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'C' and resid 132 through 136 removed outlier: 3.837A pdb=" N VAL C 135 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA C 136 " --> pdb=" O ASP C 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 132 through 136' Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 130 through 148 Processing helix chain 'D' and resid 150 through 163 removed outlier: 3.610A pdb=" N ALA D 154 " --> pdb=" O PHE D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 224 Processing helix chain 'D' and resid 275 through 284 removed outlier: 3.512A pdb=" N ILE D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 322 through 332 removed outlier: 3.521A pdb=" N LEU D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 51 through 55 Processing helix chain 'E' and resid 82 through 91 Processing helix chain 'E' and resid 130 through 148 Processing helix chain 'E' and resid 151 through 163 Processing helix chain 'E' and resid 208 through 223 Processing helix chain 'E' and resid 275 through 284 Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.530A pdb=" N GLY E 305 " --> pdb=" O GLU E 302 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER E 306 " --> pdb=" O PRO E 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 302 through 306' Processing helix chain 'E' and resid 322 through 332 removed outlier: 3.532A pdb=" N LEU E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'F' and resid 51 through 55 removed outlier: 3.796A pdb=" N SER F 55 " --> pdb=" O ARG F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 91 Processing helix chain 'F' and resid 130 through 148 Processing helix chain 'F' and resid 151 through 163 Processing helix chain 'F' and resid 208 through 223 Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 322 through 332 Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 82 through 92 Processing helix chain 'G' and resid 130 through 148 Processing helix chain 'G' and resid 151 through 163 Processing helix chain 'G' and resid 208 through 223 Processing helix chain 'G' and resid 275 through 284 Processing helix chain 'G' and resid 322 through 332 Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 82 through 92 Processing helix chain 'H' and resid 130 through 148 Processing helix chain 'H' and resid 151 through 163 Processing helix chain 'H' and resid 208 through 223 Processing helix chain 'H' and resid 275 through 284 Processing helix chain 'H' and resid 302 through 304 No H-bonds generated for 'chain 'H' and resid 302 through 304' Processing helix chain 'H' and resid 322 through 331 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 82 through 92 Processing helix chain 'I' and resid 130 through 148 Processing helix chain 'I' and resid 150 through 163 Processing helix chain 'I' and resid 164 through 171 removed outlier: 6.331A pdb=" N ARG I 169 " --> pdb=" O PHE I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 275 through 284 Processing helix chain 'I' and resid 302 through 304 No H-bonds generated for 'chain 'I' and resid 302 through 304' Processing helix chain 'I' and resid 322 through 332 Processing helix chain 'I' and resid 338 through 352 Processing helix chain 'J' and resid 47 through 70 removed outlier: 3.522A pdb=" N PHE J 55 " --> pdb=" O VAL J 51 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP J 57 " --> pdb=" O ASP J 53 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILE J 58 " --> pdb=" O GLU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 136 Processing helix chain 'J' and resid 140 through 147 removed outlier: 3.754A pdb=" N ILE J 143 " --> pdb=" O LEU J 140 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU J 147 " --> pdb=" O THR J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 152 removed outlier: 3.537A pdb=" N VAL J 151 " --> pdb=" O PRO J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 163 through 169 Processing helix chain 'J' and resid 180 through 189 Processing helix chain 'J' and resid 191 through 200 Processing helix chain 'J' and resid 211 through 222 Processing helix chain 'K' and resid 47 through 70 removed outlier: 4.201A pdb=" N ASP K 57 " --> pdb=" O ASP K 53 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILE K 58 " --> pdb=" O GLU K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 136 Processing helix chain 'K' and resid 142 through 147 removed outlier: 3.872A pdb=" N LEU K 146 " --> pdb=" O TRP K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 168 Processing helix chain 'K' and resid 180 through 189 Processing helix chain 'K' and resid 191 through 200 removed outlier: 3.567A pdb=" N PHE K 195 " --> pdb=" O SER K 191 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR K 198 " --> pdb=" O ASN K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 222 Processing helix chain 'a' and resid 9 through 33 removed outlier: 3.944A pdb=" N LEU a 13 " --> pdb=" O THR a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 45 Processing helix chain 'a' and resid 49 through 58 removed outlier: 4.128A pdb=" N LEU a 53 " --> pdb=" O ARG a 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 96 through 100 Processing helix chain 'a' and resid 115 through 121 removed outlier: 3.899A pdb=" N LYS a 119 " --> pdb=" O LEU a 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 129 through 135 Processing helix chain 'a' and resid 148 through 161 Processing helix chain 'a' and resid 195 through 212 Processing helix chain 'a' and resid 212 through 224 Processing helix chain 'a' and resid 247 through 251 Processing helix chain 'a' and resid 253 through 258 Processing helix chain 'a' and resid 285 through 290 Processing helix chain 'a' and resid 294 through 309 removed outlier: 3.910A pdb=" N ALA a 309 " --> pdb=" O GLN a 305 " (cutoff:3.500A) Processing helix chain 'a' and resid 314 through 340 removed outlier: 3.505A pdb=" N ILE a 329 " --> pdb=" O LEU a 325 " (cutoff:3.500A) Processing helix chain 'a' and resid 341 through 343 No H-bonds generated for 'chain 'a' and resid 341 through 343' Processing helix chain 'a' and resid 346 through 350 Processing helix chain 'a' and resid 359 through 364 removed outlier: 3.519A pdb=" N ASP a 364 " --> pdb=" O GLN a 360 " (cutoff:3.500A) Processing helix chain 'a' and resid 366 through 371 Processing helix chain 'a' and resid 375 through 383 removed outlier: 3.774A pdb=" N LEU a 379 " --> pdb=" O LEU a 375 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG a 380 " --> pdb=" O GLN a 376 " (cutoff:3.500A) Processing helix chain 'a' and resid 386 through 397 Processing helix chain 'a' and resid 402 through 408 removed outlier: 3.686A pdb=" N LEU a 406 " --> pdb=" O ASP a 402 " (cutoff:3.500A) Processing helix chain 'a' and resid 409 through 431 removed outlier: 3.728A pdb=" N ASP a 431 " --> pdb=" O GLU a 427 " (cutoff:3.500A) Processing helix chain 'b' and resid 33 through 48 removed outlier: 3.744A pdb=" N PHE b 37 " --> pdb=" O SER b 33 " (cutoff:3.500A) Processing helix chain 'b' and resid 115 through 120 removed outlier: 3.536A pdb=" N LEU b 118 " --> pdb=" O GLY b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 135 Processing helix chain 'b' and resid 165 through 180 Processing helix chain 'b' and resid 189 through 204 Processing helix chain 'b' and resid 208 through 216 Processing helix chain 'b' and resid 291 through 295 removed outlier: 3.901A pdb=" N VAL b 295 " --> pdb=" O PRO b 292 " (cutoff:3.500A) Processing helix chain 'b' and resid 297 through 302 removed outlier: 3.598A pdb=" N LEU b 302 " --> pdb=" O SER b 299 " (cutoff:3.500A) Processing helix chain 'b' and resid 308 through 312 removed outlier: 3.898A pdb=" N GLY b 312 " --> pdb=" O PRO b 309 " (cutoff:3.500A) Processing helix chain 'c' and resid 16 through 36 removed outlier: 3.992A pdb=" N LEU c 20 " --> pdb=" O PRO c 16 " (cutoff:3.500A) Processing helix chain 'c' and resid 63 through 73 Processing helix chain 'c' and resid 74 through 77 removed outlier: 3.529A pdb=" N GLU c 77 " --> pdb=" O PRO c 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 74 through 77' Processing helix chain 'c' and resid 108 through 121 removed outlier: 3.730A pdb=" N LEU c 112 " --> pdb=" O ASN c 108 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG c 118 " --> pdb=" O ARG c 114 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 131 Processing helix chain 'c' and resid 132 through 136 removed outlier: 3.837A pdb=" N VAL c 135 " --> pdb=" O PRO c 132 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA c 136 " --> pdb=" O ASP c 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 132 through 136' Processing helix chain 'd' and resid 51 through 55 Processing helix chain 'd' and resid 130 through 148 Processing helix chain 'd' and resid 150 through 163 removed outlier: 3.610A pdb=" N ALA d 154 " --> pdb=" O PHE d 150 " (cutoff:3.500A) Processing helix chain 'd' and resid 208 through 224 Processing helix chain 'd' and resid 275 through 284 removed outlier: 3.512A pdb=" N ILE d 279 " --> pdb=" O HIS d 275 " (cutoff:3.500A) Processing helix chain 'd' and resid 302 through 304 No H-bonds generated for 'chain 'd' and resid 302 through 304' Processing helix chain 'd' and resid 322 through 332 removed outlier: 3.521A pdb=" N LEU d 332 " --> pdb=" O ASP d 328 " (cutoff:3.500A) Processing helix chain 'd' and resid 338 through 352 Processing helix chain 'e' and resid 51 through 55 Processing helix chain 'e' and resid 82 through 91 Processing helix chain 'e' and resid 130 through 148 Processing helix chain 'e' and resid 151 through 163 Processing helix chain 'e' and resid 208 through 223 Processing helix chain 'e' and resid 275 through 284 Processing helix chain 'e' and resid 302 through 306 removed outlier: 3.530A pdb=" N GLY e 305 " --> pdb=" O GLU e 302 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER e 306 " --> pdb=" O PRO e 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 302 through 306' Processing helix chain 'e' and resid 322 through 332 removed outlier: 3.532A pdb=" N LEU e 326 " --> pdb=" O ASP e 322 " (cutoff:3.500A) Processing helix chain 'e' and resid 338 through 352 Processing helix chain 'f' and resid 51 through 55 removed outlier: 3.796A pdb=" N SER f 55 " --> pdb=" O ARG f 52 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 91 Processing helix chain 'f' and resid 130 through 148 Processing helix chain 'f' and resid 151 through 163 Processing helix chain 'f' and resid 208 through 223 Processing helix chain 'f' and resid 275 through 284 Processing helix chain 'f' and resid 302 through 304 No H-bonds generated for 'chain 'f' and resid 302 through 304' Processing helix chain 'f' and resid 322 through 332 Processing helix chain 'f' and resid 338 through 352 Processing helix chain 'g' and resid 82 through 92 Processing helix chain 'g' and resid 130 through 148 Processing helix chain 'g' and resid 151 through 163 Processing helix chain 'g' and resid 208 through 223 Processing helix chain 'g' and resid 275 through 284 Processing helix chain 'g' and resid 322 through 332 Processing helix chain 'g' and resid 338 through 352 Processing helix chain 'h' and resid 82 through 92 Processing helix chain 'h' and resid 130 through 148 Processing helix chain 'h' and resid 151 through 163 Processing helix chain 'h' and resid 208 through 223 Processing helix chain 'h' and resid 275 through 284 Processing helix chain 'h' and resid 302 through 304 No H-bonds generated for 'chain 'h' and resid 302 through 304' Processing helix chain 'h' and resid 322 through 331 Processing helix chain 'h' and resid 338 through 352 Processing helix chain 'i' and resid 82 through 92 Processing helix chain 'i' and resid 130 through 148 Processing helix chain 'i' and resid 150 through 163 Processing helix chain 'i' and resid 164 through 171 removed outlier: 6.331A pdb=" N ARG i 169 " --> pdb=" O PHE i 166 " (cutoff:3.500A) Processing helix chain 'i' and resid 208 through 224 Processing helix chain 'i' and resid 275 through 284 Processing helix chain 'i' and resid 302 through 304 No H-bonds generated for 'chain 'i' and resid 302 through 304' Processing helix chain 'i' and resid 322 through 332 Processing helix chain 'i' and resid 338 through 352 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 removed outlier: 5.658A pdb=" N GLY B 285 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLY B 287 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP B 316 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 240 removed outlier: 4.221A pdb=" N PHE B 81 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 267 removed outlier: 5.780A pdb=" N LEU A 265 " --> pdb=" O TRP B 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 55 through 61 removed outlier: 3.891A pdb=" N VAL B 59 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU B 110 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE B 61 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER B 108 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU B 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN B 18 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL B 107 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER B 16 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LEU B 109 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ARG B 14 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU B 111 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU B 12 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL B 113 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 10 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 68 removed outlier: 4.821A pdb=" N LEU B 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN B 18 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL B 107 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER B 16 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LEU B 109 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ARG B 14 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU B 111 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU B 12 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL B 113 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 10 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 220 through 222 removed outlier: 4.696A pdb=" N ASN B 220 " --> pdb=" O ARG B 242 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AB2, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AB3, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AB4, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB5, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AB6, first strand: chain 'D' and resid 38 through 39 removed outlier: 3.880A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU D 229 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL D 177 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ASP D 196 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL D 179 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG D 194 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE D 181 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA D 192 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS D 183 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB8, first strand: chain 'D' and resid 46 through 47 Processing sheet with id=AB9, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AC1, first strand: chain 'D' and resid 248 through 249 removed outlier: 3.771A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AC3, first strand: chain 'D' and resid 306 through 307 removed outlier: 3.575A pdb=" N LYS D 312 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 127 through 128 removed outlier: 3.806A pdb=" N PHE E 355 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 38 through 39 removed outlier: 3.829A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL E 179 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ARG E 194 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AC7, first strand: chain 'E' and resid 63 through 70 removed outlier: 4.513A pdb=" N ALA E 101 " --> pdb=" O VAL E 244 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 285 through 287 Processing sheet with id=AC9, first strand: chain 'F' and resid 31 through 32 Processing sheet with id=AD1, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.911A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL F 177 " --> pdb=" O ASP F 196 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASP F 196 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL F 179 " --> pdb=" O ARG F 194 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG F 194 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE F 181 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA F 192 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N HIS F 183 " --> pdb=" O ALA F 190 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=AD3, first strand: chain 'F' and resid 64 through 70 Processing sheet with id=AD4, first strand: chain 'F' and resid 285 through 287 Processing sheet with id=AD5, first strand: chain 'F' and resid 306 through 307 removed outlier: 3.672A pdb=" N LYS F 312 " --> pdb=" O VAL F 307 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 31 through 33 Processing sheet with id=AD7, first strand: chain 'G' and resid 38 through 39 removed outlier: 3.899A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL G 177 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASP G 196 " --> pdb=" O VAL G 177 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL G 179 " --> pdb=" O ARG G 194 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG G 194 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE G 181 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA G 192 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N HIS G 183 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AD9, first strand: chain 'G' and resid 63 through 70 removed outlier: 4.377A pdb=" N ALA G 101 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 285 through 287 Processing sheet with id=AE2, first strand: chain 'H' and resid 127 through 128 removed outlier: 3.983A pdb=" N PHE H 355 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 188 through 196 removed outlier: 6.472A pdb=" N HIS H 183 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA H 192 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE H 181 " --> pdb=" O ALA H 192 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG H 194 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL H 179 " --> pdb=" O ARG H 194 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASP H 196 " --> pdb=" O VAL H 177 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL H 177 " --> pdb=" O ASP H 196 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 63 through 70 removed outlier: 3.823A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA H 101 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 63 through 70 removed outlier: 3.823A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS H 261 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR H 97 " --> pdb=" O LYS H 261 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS H 263 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU H 265 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N ALA H 101 " --> pdb=" O LEU H 265 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR H 264 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 285 through 287 Processing sheet with id=AE7, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.944A pdb=" N VAL H 307 " --> pdb=" O LYS H 312 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.698A pdb=" N GLY I 353 " --> pdb=" O PHE I 33 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 38 through 39 removed outlier: 3.523A pdb=" N ARG I 117 " --> pdb=" O ASP I 38 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL I 177 " --> pdb=" O ASP I 196 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASP I 196 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL I 179 " --> pdb=" O ARG I 194 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG I 194 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE I 181 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA I 192 " --> pdb=" O ILE I 181 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS I 183 " --> pdb=" O ALA I 190 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 38 through 39 removed outlier: 3.523A pdb=" N ARG I 117 " --> pdb=" O ASP I 38 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.945A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 243 through 244 removed outlier: 4.575A pdb=" N ALA I 101 " --> pdb=" O VAL I 244 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N THR J 12 " --> pdb=" O TYR J 31 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N TYR J 31 " --> pdb=" O THR J 12 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ALA J 14 " --> pdb=" O THR J 29 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N THR J 29 " --> pdb=" O ALA J 14 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG J 16 " --> pdb=" O GLN J 27 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN J 27 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N HIS J 26 " --> pdb=" O THR J 41 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR J 41 " --> pdb=" O HIS J 26 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP J 28 " --> pdb=" O ILE J 39 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE J 39 " --> pdb=" O TRP J 28 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU J 30 " --> pdb=" O MET J 37 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AF5, first strand: chain 'I' and resid 306 through 307 removed outlier: 3.524A pdb=" N VAL I 307 " --> pdb=" O LYS I 312 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS I 312 " --> pdb=" O VAL I 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'J' and resid 85 through 91 removed outlier: 3.603A pdb=" N ASP J 73 " --> pdb=" O VAL J 91 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU J 119 " --> pdb=" O THR J 113 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER J 99 " --> pdb=" O GLY J 120 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 4 through 6 removed outlier: 4.220A pdb=" N ALA K 38 " --> pdb=" O LEU K 30 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N TYR K 32 " --> pdb=" O GLU K 36 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU K 36 " --> pdb=" O TYR K 32 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 19 through 20 removed outlier: 5.782A pdb=" N HIS K 19 " --> pdb=" O LEU i 95 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N THR i 97 " --> pdb=" O HIS K 19 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN i 94 " --> pdb=" O GLY i 70 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 19 through 20 removed outlier: 5.782A pdb=" N HIS K 19 " --> pdb=" O LEU i 95 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N THR i 97 " --> pdb=" O HIS K 19 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA i 101 " --> pdb=" O VAL i 244 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 85 through 90 removed outlier: 5.362A pdb=" N LEU K 119 " --> pdb=" O THR K 113 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 64 through 66 Processing sheet with id=AG3, first strand: chain 'a' and resid 94 through 95 Processing sheet with id=AG4, first strand: chain 'a' and resid 94 through 95 removed outlier: 5.658A pdb=" N GLY b 285 " --> pdb=" O PRO b 252 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLY b 287 " --> pdb=" O PRO b 250 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ALA b 253 " --> pdb=" O TRP b 316 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP b 316 " --> pdb=" O ALA b 253 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'a' and resid 180 through 181 Processing sheet with id=AG6, first strand: chain 'a' and resid 239 through 240 removed outlier: 4.221A pdb=" N PHE b 81 " --> pdb=" O ILE a 240 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'a' and resid 265 through 267 removed outlier: 5.780A pdb=" N LEU a 265 " --> pdb=" O TRP b 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'b' and resid 55 through 61 removed outlier: 3.891A pdb=" N VAL b 59 " --> pdb=" O LEU b 110 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU b 110 " --> pdb=" O VAL b 59 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE b 61 " --> pdb=" O SER b 108 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER b 108 " --> pdb=" O ILE b 61 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU b 105 " --> pdb=" O GLN b 18 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN b 18 " --> pdb=" O LEU b 105 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL b 107 " --> pdb=" O SER b 16 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N SER b 16 " --> pdb=" O VAL b 107 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N LEU b 109 " --> pdb=" O ARG b 14 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ARG b 14 " --> pdb=" O LEU b 109 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU b 111 " --> pdb=" O LEU b 12 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU b 12 " --> pdb=" O LEU b 111 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL b 113 " --> pdb=" O LEU b 10 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU b 10 " --> pdb=" O VAL b 113 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER b 16 " --> pdb=" O LEU b 145 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 65 through 68 removed outlier: 4.821A pdb=" N LEU b 105 " --> pdb=" O GLN b 18 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN b 18 " --> pdb=" O LEU b 105 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL b 107 " --> pdb=" O SER b 16 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N SER b 16 " --> pdb=" O VAL b 107 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N LEU b 109 " --> pdb=" O ARG b 14 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ARG b 14 " --> pdb=" O LEU b 109 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU b 111 " --> pdb=" O LEU b 12 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU b 12 " --> pdb=" O LEU b 111 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL b 113 " --> pdb=" O LEU b 10 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU b 10 " --> pdb=" O VAL b 113 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'b' and resid 220 through 222 removed outlier: 4.695A pdb=" N ASN b 220 " --> pdb=" O ARG b 242 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'c' and resid 41 through 43 Processing sheet with id=AH3, first strand: chain 'c' and resid 41 through 43 Processing sheet with id=AH4, first strand: chain 'c' and resid 97 through 98 Processing sheet with id=AH5, first strand: chain 'c' and resid 100 through 102 Processing sheet with id=AH6, first strand: chain 'd' and resid 127 through 128 Processing sheet with id=AH7, first strand: chain 'd' and resid 38 through 39 removed outlier: 3.880A pdb=" N VAL d 228 " --> pdb=" O VAL d 118 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU d 229 " --> pdb=" O ILE d 184 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL d 177 " --> pdb=" O ASP d 196 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ASP d 196 " --> pdb=" O VAL d 177 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL d 179 " --> pdb=" O ARG d 194 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG d 194 " --> pdb=" O VAL d 179 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE d 181 " --> pdb=" O ALA d 192 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA d 192 " --> pdb=" O ILE d 181 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HIS d 183 " --> pdb=" O ALA d 190 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'd' and resid 42 through 43 Processing sheet with id=AH9, first strand: chain 'd' and resid 46 through 47 Processing sheet with id=AI1, first strand: chain 'd' and resid 64 through 66 Processing sheet with id=AI2, first strand: chain 'd' and resid 248 through 249 removed outlier: 3.771A pdb=" N THR d 264 " --> pdb=" O GLU d 249 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'd' and resid 285 through 287 Processing sheet with id=AI4, first strand: chain 'd' and resid 306 through 307 removed outlier: 3.575A pdb=" N LYS d 312 " --> pdb=" O VAL d 307 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'e' and resid 127 through 128 removed outlier: 3.806A pdb=" N PHE e 355 " --> pdb=" O LEU e 31 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'e' and resid 38 through 39 removed outlier: 3.828A pdb=" N VAL e 228 " --> pdb=" O VAL e 118 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU e 229 " --> pdb=" O ILE e 184 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL e 179 " --> pdb=" O ARG e 194 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ARG e 194 " --> pdb=" O VAL e 179 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE e 181 " --> pdb=" O ALA e 192 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA e 192 " --> pdb=" O ILE e 181 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N HIS e 183 " --> pdb=" O ALA e 190 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'e' and resid 38 through 39 Processing sheet with id=AI8, first strand: chain 'e' and resid 63 through 70 removed outlier: 4.513A pdb=" N ALA e 101 " --> pdb=" O VAL e 244 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'e' and resid 285 through 287 Processing sheet with id=AJ1, first strand: chain 'f' and resid 31 through 32 Processing sheet with id=AJ2, first strand: chain 'f' and resid 38 through 39 removed outlier: 3.912A pdb=" N VAL f 228 " --> pdb=" O VAL f 118 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU f 229 " --> pdb=" O ILE f 184 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL f 177 " --> pdb=" O ASP f 196 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP f 196 " --> pdb=" O VAL f 177 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL f 179 " --> pdb=" O ARG f 194 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG f 194 " --> pdb=" O VAL f 179 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE f 181 " --> pdb=" O ALA f 192 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ALA f 192 " --> pdb=" O ILE f 181 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N HIS f 183 " --> pdb=" O ALA f 190 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'f' and resid 38 through 39 Processing sheet with id=AJ4, first strand: chain 'f' and resid 64 through 70 Processing sheet with id=AJ5, first strand: chain 'f' and resid 285 through 287 Processing sheet with id=AJ6, first strand: chain 'f' and resid 306 through 307 removed outlier: 3.672A pdb=" N LYS f 312 " --> pdb=" O VAL f 307 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'g' and resid 31 through 33 Processing sheet with id=AJ8, first strand: chain 'g' and resid 38 through 39 removed outlier: 3.899A pdb=" N VAL g 228 " --> pdb=" O VAL g 118 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU g 229 " --> pdb=" O ILE g 184 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL g 177 " --> pdb=" O ASP g 196 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASP g 196 " --> pdb=" O VAL g 177 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL g 179 " --> pdb=" O ARG g 194 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG g 194 " --> pdb=" O VAL g 179 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE g 181 " --> pdb=" O ALA g 192 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA g 192 " --> pdb=" O ILE g 181 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N HIS g 183 " --> pdb=" O ALA g 190 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'g' and resid 38 through 39 Processing sheet with id=AK1, first strand: chain 'g' and resid 63 through 70 removed outlier: 4.377A pdb=" N ALA g 101 " --> pdb=" O VAL g 244 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'g' and resid 285 through 287 Processing sheet with id=AK3, first strand: chain 'h' and resid 127 through 128 removed outlier: 3.983A pdb=" N PHE h 355 " --> pdb=" O LEU h 31 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'h' and resid 188 through 196 removed outlier: 6.472A pdb=" N HIS h 183 " --> pdb=" O ALA h 190 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA h 192 " --> pdb=" O ILE h 181 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE h 181 " --> pdb=" O ALA h 192 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG h 194 " --> pdb=" O VAL h 179 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL h 179 " --> pdb=" O ARG h 194 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASP h 196 " --> pdb=" O VAL h 177 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL h 177 " --> pdb=" O ASP h 196 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU h 229 " --> pdb=" O ILE h 184 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL h 228 " --> pdb=" O VAL h 118 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'h' and resid 63 through 70 removed outlier: 3.824A pdb=" N ASN h 94 " --> pdb=" O GLY h 70 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA h 101 " --> pdb=" O VAL h 244 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'h' and resid 63 through 70 removed outlier: 3.824A pdb=" N ASN h 94 " --> pdb=" O GLY h 70 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS h 261 " --> pdb=" O LEU h 95 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR h 97 " --> pdb=" O LYS h 261 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS h 263 " --> pdb=" O THR h 97 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU h 265 " --> pdb=" O ASP h 99 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N ALA h 101 " --> pdb=" O LEU h 265 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR h 264 " --> pdb=" O GLU h 249 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'h' and resid 285 through 287 Processing sheet with id=AK8, first strand: chain 'h' and resid 306 through 307 removed outlier: 3.944A pdb=" N VAL h 307 " --> pdb=" O LYS h 312 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS h 312 " --> pdb=" O VAL h 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK8 Processing sheet with id=AK9, first strand: chain 'i' and resid 127 through 128 removed outlier: 3.699A pdb=" N GLY i 353 " --> pdb=" O PHE i 33 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'i' and resid 38 through 39 removed outlier: 3.523A pdb=" N ARG i 117 " --> pdb=" O ASP i 38 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU i 229 " --> pdb=" O ILE i 184 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL i 177 " --> pdb=" O ASP i 196 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASP i 196 " --> pdb=" O VAL i 177 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL i 179 " --> pdb=" O ARG i 194 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG i 194 " --> pdb=" O VAL i 179 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE i 181 " --> pdb=" O ALA i 192 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA i 192 " --> pdb=" O ILE i 181 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N HIS i 183 " --> pdb=" O ALA i 190 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'i' and resid 38 through 39 removed outlier: 3.523A pdb=" N ARG i 117 " --> pdb=" O ASP i 38 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'i' and resid 285 through 287 Processing sheet with id=AL4, first strand: chain 'i' and resid 306 through 307 removed outlier: 3.524A pdb=" N VAL i 307 " --> pdb=" O LYS i 312 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS i 312 " --> pdb=" O VAL i 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL4 2099 hydrogen bonds defined for protein. 5748 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 20.69 Time building geometry restraints manager: 21.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10062 1.33 - 1.45: 12948 1.45 - 1.57: 28578 1.57 - 1.69: 242 1.69 - 1.81: 90 Bond restraints: 51920 Sorted by residual: bond pdb=" C ARG K 116 " pdb=" O ARG K 116 " ideal model delta sigma weight residual 1.244 1.205 0.039 9.40e-03 1.13e+04 1.68e+01 bond pdb=" C LEU b 181 " pdb=" N PRO b 182 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.45e+00 bond pdb=" C LEU B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.39e+00 bond pdb=" CA SER K 92 " pdb=" C SER K 92 " ideal model delta sigma weight residual 1.525 1.502 0.023 1.29e-02 6.01e+03 3.20e+00 bond pdb=" N ARG K 116 " pdb=" CA ARG K 116 " ideal model delta sigma weight residual 1.462 1.448 0.014 7.70e-03 1.69e+04 3.16e+00 ... (remaining 51915 not shown) Histogram of bond angle deviations from ideal: 94.00 - 102.25: 169 102.25 - 110.49: 14645 110.49 - 118.74: 27673 118.74 - 126.98: 27653 126.98 - 135.23: 982 Bond angle restraints: 71122 Sorted by residual: angle pdb=" N SER K 92 " pdb=" CA SER K 92 " pdb=" C SER K 92 " ideal model delta sigma weight residual 112.04 105.15 6.89 1.44e+00 4.82e-01 2.29e+01 angle pdb=" N PRO K 34 " pdb=" CA PRO K 34 " pdb=" C PRO K 34 " ideal model delta sigma weight residual 114.68 109.78 4.90 1.04e+00 9.25e-01 2.22e+01 angle pdb=" C LYS G 77 " pdb=" N THR G 78 " pdb=" CA THR G 78 " ideal model delta sigma weight residual 121.54 130.20 -8.66 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C LYS g 77 " pdb=" N THR g 78 " pdb=" CA THR g 78 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 angle pdb=" C ARG K 116 " pdb=" N PRO K 117 " pdb=" CA PRO K 117 " ideal model delta sigma weight residual 119.84 114.57 5.27 1.25e+00 6.40e-01 1.78e+01 ... (remaining 71117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 30030 35.78 - 71.56: 784 71.56 - 107.33: 48 107.33 - 143.11: 2 143.11 - 178.89: 12 Dihedral angle restraints: 30876 sinusoidal: 12900 harmonic: 17976 Sorted by residual: dihedral pdb=" O4' U m 33 " pdb=" C1' U m 33 " pdb=" N1 U m 33 " pdb=" C2 U m 33 " ideal model delta sinusoidal sigma weight residual 200.00 52.41 147.59 1 1.50e+01 4.44e-03 7.87e+01 dihedral pdb=" O4' U M 33 " pdb=" C1' U M 33 " pdb=" N1 U M 33 " pdb=" C2 U M 33 " ideal model delta sinusoidal sigma weight residual 200.00 52.46 147.54 1 1.50e+01 4.44e-03 7.87e+01 dihedral pdb=" O4' U m 21 " pdb=" C1' U m 21 " pdb=" N1 U m 21 " pdb=" C2 U m 21 " ideal model delta sinusoidal sigma weight residual 200.00 52.68 147.32 1 1.50e+01 4.44e-03 7.86e+01 ... (remaining 30873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 6933 0.066 - 0.132: 995 0.132 - 0.197: 65 0.197 - 0.263: 14 0.263 - 0.329: 5 Chirality restraints: 8012 Sorted by residual: chirality pdb=" CB ILE e 72 " pdb=" CA ILE e 72 " pdb=" CG1 ILE e 72 " pdb=" CG2 ILE e 72 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB ILE E 72 " pdb=" CA ILE E 72 " pdb=" CG1 ILE E 72 " pdb=" CG2 ILE E 72 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB ILE K 6 " pdb=" CA ILE K 6 " pdb=" CG1 ILE K 6 " pdb=" CG2 ILE K 6 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 8009 not shown) Planarity restraints: 8928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP f 82 " 0.086 5.00e-02 4.00e+02 1.27e-01 2.60e+01 pdb=" N PRO f 83 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO f 83 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO f 83 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 82 " 0.085 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO F 83 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO F 83 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO F 83 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 71 " 0.054 5.00e-02 4.00e+02 8.12e-02 1.05e+01 pdb=" N PRO A 72 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.045 5.00e-02 4.00e+02 ... (remaining 8925 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 6736 2.76 - 3.29: 46993 3.29 - 3.83: 91755 3.83 - 4.36: 109541 4.36 - 4.90: 181211 Nonbonded interactions: 436236 Sorted by model distance: nonbonded pdb=" CD2 LEU K 119 " pdb=" OE1 GLN g 91 " model vdw 2.223 3.460 nonbonded pdb=" OH TYR g 290 " pdb=" O GLY g 297 " model vdw 2.243 2.440 nonbonded pdb=" OH TYR G 290 " pdb=" O GLY G 297 " model vdw 2.244 2.440 nonbonded pdb=" O ALA J 141 " pdb=" OG1 THR J 144 " model vdw 2.266 2.440 nonbonded pdb=" OG SER b 24 " pdb=" O PHE b 31 " model vdw 2.282 2.440 ... (remaining 436231 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = (chain 'C' and (resid 1 through 174 or resid 176 through 187)) selection = (chain 'c' and (resid 1 through 174 or resid 176 through 187)) } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'F' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'G' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'H' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'I' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = chain 'd' selection = (chain 'e' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'f' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'g' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'h' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'i' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) } ncs_group { reference = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 120 5.49 5 S 58 5.16 5 C 31428 2.51 5 N 9208 2.21 5 O 9806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 9.600 Check model and map are aligned: 0.780 Convert atoms to be neutral: 0.470 Process input model: 137.400 Find NCS groups from input model: 3.400 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 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 : 0.004 0.072 51920 Z= 0.238 Angle : 0.745 12.205 71122 Z= 0.403 Chirality : 0.046 0.329 8012 Planarity : 0.007 0.127 8928 Dihedral : 16.231 178.888 19268 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.98 % Favored : 95.01 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.09), residues: 6192 helix: -1.29 (0.09), residues: 1960 sheet: 0.41 (0.17), residues: 966 loop : -1.83 (0.10), residues: 3266 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1170 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1145 time to evaluate : 6.001 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 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 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: 25 outliers final: 5 residues processed: 1162 average time/residue: 0.6512 time to fit residues: 1223.1552 Evaluate side-chains 572 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 567 time to evaluate : 5.740 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5634 time to fit residues: 12.1540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 526 optimal weight: 9.9990 chunk 472 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 319 optimal weight: 6.9990 chunk 252 optimal weight: 3.9990 chunk 489 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 297 optimal weight: 2.9990 chunk 364 optimal weight: 9.9990 chunk 566 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 HIS ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS D 186 GLN D 227 HIS ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 GLN E 148 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 GLN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 HIS I 348 ASN J 194 ASN ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 188 HIS a 203 HIS ** a 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 HIS d 159 HIS d 329 ASN ** e 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 342 GLN ** f 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 160 ASN f 182 ASN f 310 GLN ** f 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 94 ASN ** h 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 51920 Z= 0.264 Angle : 0.652 14.489 71122 Z= 0.334 Chirality : 0.042 0.249 8012 Planarity : 0.005 0.074 8928 Dihedral : 11.457 178.610 8276 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 3.17 % 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: -0.79 (0.10), residues: 6192 helix: 0.33 (0.11), residues: 1958 sheet: 0.95 (0.17), residues: 912 loop : -1.52 (0.10), residues: 3322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 602 time to evaluate : 5.807 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 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: 154 outliers final: 68 residues processed: 699 average time/residue: 0.6358 time to fit residues: 751.1307 Evaluate side-chains 535 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 467 time to evaluate : 5.769 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.4614 time to fit residues: 66.6385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 314 optimal weight: 7.9990 chunk 175 optimal weight: 0.0030 chunk 471 optimal weight: 20.0000 chunk 385 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 567 optimal weight: 9.9990 chunk 613 optimal weight: 4.9990 chunk 505 optimal weight: 7.9990 chunk 562 optimal weight: 30.0000 chunk 193 optimal weight: 3.9990 chunk 455 optimal weight: 5.9990 overall best weight: 3.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 281 ASN J 25 HIS J 154 HIS ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 306 HIS d 129 ASN ** d 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 348 ASN ** f 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 281 ASN f 310 GLN ** f 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 96 GLN h 310 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 51920 Z= 0.285 Angle : 0.633 12.919 71122 Z= 0.323 Chirality : 0.042 0.314 8012 Planarity : 0.005 0.059 8928 Dihedral : 11.353 178.168 8276 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.11), residues: 6192 helix: 0.81 (0.11), residues: 1982 sheet: 0.90 (0.17), residues: 940 loop : -1.38 (0.11), residues: 3270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 526 time to evaluate : 5.742 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 134 outliers final: 57 residues processed: 625 average time/residue: 0.5869 time to fit residues: 620.7324 Evaluate side-chains 480 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 423 time to evaluate : 5.842 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.4525 time to fit residues: 55.1957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 560 optimal weight: 6.9990 chunk 426 optimal weight: 6.9990 chunk 294 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 270 optimal weight: 7.9990 chunk 381 optimal weight: 9.9990 chunk 569 optimal weight: 10.0000 chunk 603 optimal weight: 10.0000 chunk 297 optimal weight: 0.5980 chunk 539 optimal weight: 20.0000 chunk 162 optimal weight: 2.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 81 ASN ** a 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 51920 Z= 0.245 Angle : 0.605 12.492 71122 Z= 0.308 Chirality : 0.041 0.221 8012 Planarity : 0.004 0.061 8928 Dihedral : 11.300 177.988 8276 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer Outliers : 2.00 % 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: -0.23 (0.11), residues: 6192 helix: 1.12 (0.11), residues: 1980 sheet: 0.92 (0.17), residues: 952 loop : -1.35 (0.11), residues: 3260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 492 time to evaluate : 5.771 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: 97 outliers final: 32 residues processed: 555 average time/residue: 0.6006 time to fit residues: 565.8641 Evaluate side-chains 435 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 403 time to evaluate : 5.569 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.4512 time to fit residues: 34.2250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 502 optimal weight: 0.0000 chunk 342 optimal weight: 30.0000 chunk 8 optimal weight: 8.9990 chunk 449 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 514 optimal weight: 3.9990 chunk 416 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 307 optimal weight: 0.6980 chunk 541 optimal weight: 7.9990 chunk 152 optimal weight: 7.9990 overall best weight: 2.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 306 HIS ** d 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 310 GLN ** h 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 51920 Z= 0.224 Angle : 0.596 12.570 71122 Z= 0.301 Chirality : 0.041 0.275 8012 Planarity : 0.004 0.061 8928 Dihedral : 11.273 178.038 8276 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 1.59 % 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: -0.15 (0.11), residues: 6192 helix: 1.26 (0.12), residues: 1980 sheet: 0.89 (0.17), residues: 962 loop : -1.33 (0.11), residues: 3250 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 456 time to evaluate : 5.744 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: 77 outliers final: 30 residues processed: 504 average time/residue: 0.6013 time to fit residues: 515.0120 Evaluate side-chains 443 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 413 time to evaluate : 6.215 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.5272 time to fit residues: 38.8260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 202 optimal weight: 6.9990 chunk 543 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 354 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 603 optimal weight: 20.0000 chunk 501 optimal weight: 4.9990 chunk 279 optimal weight: 0.0470 chunk 50 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 316 optimal weight: 1.9990 overall best weight: 1.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 81 ASN ** a 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 51920 Z= 0.177 Angle : 0.578 13.766 71122 Z= 0.289 Chirality : 0.040 0.344 8012 Planarity : 0.004 0.060 8928 Dihedral : 11.232 179.281 8276 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.11), residues: 6192 helix: 1.39 (0.12), residues: 1982 sheet: 0.94 (0.17), residues: 960 loop : -1.32 (0.11), residues: 3250 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 466 time to evaluate : 5.587 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: 46 outliers final: 15 residues processed: 493 average time/residue: 0.5923 time to fit residues: 496.3672 Evaluate side-chains 437 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 422 time to evaluate : 5.384 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.4635 time to fit residues: 20.1991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 582 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 343 optimal weight: 20.0000 chunk 440 optimal weight: 20.0000 chunk 341 optimal weight: 10.0000 chunk 508 optimal weight: 10.0000 chunk 337 optimal weight: 8.9990 chunk 601 optimal weight: 9.9990 chunk 376 optimal weight: 5.9990 chunk 366 optimal weight: 6.9990 chunk 277 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN B 114 HIS ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 242 GLN ** I 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 HIS ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 216 HIS ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 69 GLN b 89 ASN ** b 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 306 HIS ** d 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 260 GLN ** g 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 183 HIS ** i 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.073 51920 Z= 0.512 Angle : 0.805 15.457 71122 Z= 0.408 Chirality : 0.045 0.328 8012 Planarity : 0.006 0.081 8928 Dihedral : 11.624 179.594 8276 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 26.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % 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: -0.45 (0.11), residues: 6192 helix: 0.97 (0.11), residues: 1954 sheet: 0.65 (0.17), residues: 1006 loop : -1.47 (0.11), residues: 3232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 400 time to evaluate : 5.786 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: 90 outliers final: 44 residues processed: 457 average time/residue: 0.6194 time to fit residues: 483.7051 Evaluate side-chains 396 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 352 time to evaluate : 5.778 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.5063 time to fit residues: 47.7962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 372 optimal weight: 7.9990 chunk 240 optimal weight: 0.1980 chunk 359 optimal weight: 4.9990 chunk 181 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 382 optimal weight: 5.9990 chunk 409 optimal weight: 50.0000 chunk 297 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 472 optimal weight: 5.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 183 HIS ** d 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 348 ASN h 163 ASN i 348 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 51920 Z= 0.205 Angle : 0.626 14.047 71122 Z= 0.314 Chirality : 0.041 0.259 8012 Planarity : 0.004 0.063 8928 Dihedral : 11.391 179.073 8276 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.25 % Favored : 94.73 % Rotamer Outliers : 0.78 % 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: -0.14 (0.11), residues: 6192 helix: 1.31 (0.12), residues: 1942 sheet: 0.75 (0.17), residues: 950 loop : -1.26 (0.11), residues: 3300 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 426 time to evaluate : 6.320 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: 38 outliers final: 18 residues processed: 450 average time/residue: 0.6017 time to fit residues: 470.8277 Evaluate side-chains 393 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 375 time to evaluate : 5.843 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4662 time to fit residues: 24.0402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 547 optimal weight: 10.0000 chunk 576 optimal weight: 0.0570 chunk 525 optimal weight: 0.9980 chunk 560 optimal weight: 1.9990 chunk 337 optimal weight: 40.0000 chunk 244 optimal weight: 3.9990 chunk 440 optimal weight: 20.0000 chunk 171 optimal weight: 0.9980 chunk 506 optimal weight: 8.9990 chunk 530 optimal weight: 5.9990 chunk 558 optimal weight: 4.9990 overall best weight: 1.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 348 ASN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 157 GLN ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 306 HIS ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 51920 Z= 0.189 Angle : 0.623 13.713 71122 Z= 0.309 Chirality : 0.041 0.258 8012 Planarity : 0.004 0.058 8928 Dihedral : 11.293 178.597 8276 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.67 % Favored : 94.31 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.11), residues: 6192 helix: 1.41 (0.12), residues: 1944 sheet: 0.82 (0.17), residues: 948 loop : -1.22 (0.11), residues: 3300 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 420 time to evaluate : 5.696 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 outliers start: 36 outliers final: 15 residues processed: 437 average time/residue: 0.6251 time to fit residues: 466.3827 Evaluate side-chains 399 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 384 time to evaluate : 6.155 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.5198 time to fit residues: 22.3581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 368 optimal weight: 2.9990 chunk 592 optimal weight: 8.9990 chunk 361 optimal weight: 10.0000 chunk 281 optimal weight: 5.9990 chunk 411 optimal weight: 50.0000 chunk 621 optimal weight: 20.0000 chunk 572 optimal weight: 30.0000 chunk 495 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 382 optimal weight: 7.9990 chunk 303 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 102 ASN ** g 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 51920 Z= 0.359 Angle : 0.683 13.845 71122 Z= 0.344 Chirality : 0.043 0.315 8012 Planarity : 0.005 0.063 8928 Dihedral : 11.386 178.235 8276 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer Outliers : 0.35 % 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: -0.14 (0.11), residues: 6192 helix: 1.32 (0.12), residues: 1942 sheet: 0.69 (0.17), residues: 974 loop : -1.27 (0.11), residues: 3276 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 385 time to evaluate : 5.349 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 outliers start: 17 outliers final: 8 residues processed: 390 average time/residue: 0.6123 time to fit residues: 409.5097 Evaluate side-chains 381 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 373 time to evaluate : 5.924 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4674 time to fit residues: 14.8525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 393 optimal weight: 0.0980 chunk 527 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 456 optimal weight: 4.9990 chunk 73 optimal weight: 30.0000 chunk 137 optimal weight: 8.9990 chunk 495 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 509 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** D 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 306 HIS ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.100190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.073152 restraints weight = 237556.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.075112 restraints weight = 113263.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.076302 restraints weight = 70206.099| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3900 r_free = 0.3900 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3899 r_free = 0.3899 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.088 51920 Z= 0.185 Angle : 0.632 15.893 71122 Z= 0.313 Chirality : 0.041 0.329 8012 Planarity : 0.004 0.060 8928 Dihedral : 11.299 178.129 8276 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer Outliers : 0.43 % 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: -0.03 (0.11), residues: 6192 helix: 1.42 (0.12), residues: 1944 sheet: 0.79 (0.17), residues: 938 loop : -1.19 (0.11), residues: 3310 =============================================================================== Job complete usr+sys time: 10761.37 seconds wall clock time: 195 minutes 27.55 seconds (11727.55 seconds total)