Starting phenix.real_space_refine (version: dev) on Sat Feb 25 03:03:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caj_23209/02_2023/6caj_23209_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caj_23209/02_2023/6caj_23209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caj_23209/02_2023/6caj_23209.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caj_23209/02_2023/6caj_23209.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caj_23209/02_2023/6caj_23209_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caj_23209/02_2023/6caj_23209_updated.pdb" } resolution = 2.8 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= 0.003 sd= 0.073 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 Process input model Symmetric amino acids flipped Residue "B ARG 55": "NH1" <-> "NH2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 234": "NH1" <-> "NH2" Residue "H ARG 108": "NH1" <-> "NH2" Residue "H PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "F ARG 321": "NH1" <-> "NH2" Residue "F ARG 374": "NH1" <-> "NH2" Residue "F ARG 417": "NH1" <-> "NH2" Residue "F ARG 467": "NH1" <-> "NH2" Residue "A ARG 55": "NH1" <-> "NH2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 234": "NH1" <-> "NH2" Residue "G ARG 108": "NH1" <-> "NH2" Residue "G PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "D PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E ARG 321": "NH1" <-> "NH2" Residue "E ARG 374": "NH1" <-> "NH2" Residue "E ARG 417": "NH1" <-> "NH2" Residue "E ARG 467": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 24295 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3201 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 402} Chain breaks: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 85 Chain: "J" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1753 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 11, 'TRANS': 232} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 94 Chain: "H" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1916 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 3 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2472 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2776 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 338} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3201 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 402} Chain breaks: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 85 Chain: "I" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1753 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 11, 'TRANS': 232} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 94 Chain: "G" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1916 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 3 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "D" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2472 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2775 Classifications: {'peptide': 357} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 338} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 60 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 30 Unusual residues: {'C7B': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 30 Unusual residues: {'C7B': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C09AC7B C 401 " occ=0.50 ... (58 atoms not shown) pdb="CL2 BC7B C 401 " occ=0.50 Time building chain proxies: 13.19, per 1000 atoms: 0.54 Number of scatterers: 24295 At special positions: 0 Unit cell: (135.27, 172.01, 118.57, 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) Cl 4 17.00 S 122 16.00 O 4470 8.00 N 4238 7.00 C 15461 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: 9.86 Conformation dependent library (CDL) restraints added in 3.7 seconds 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6090 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 40 sheets defined 36.7% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 99 through 107 Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 131 through 141 Processing helix chain 'B' and resid 162 through 175 Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 269 through 277 Processing helix chain 'B' and resid 303 through 314 Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'J' and resid 36 through 45 removed outlier: 3.831A pdb=" N LEU J 40 " --> pdb=" O ILE J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 69 removed outlier: 4.140A pdb=" N MET J 69 " --> pdb=" O ALA J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 92 Processing helix chain 'J' and resid 94 through 96 No H-bonds generated for 'chain 'J' and resid 94 through 96' Processing helix chain 'J' and resid 115 through 123 Processing helix chain 'J' and resid 184 through 189 Processing helix chain 'J' and resid 209 through 217 Processing helix chain 'J' and resid 284 through 287 No H-bonds generated for 'chain 'J' and resid 284 through 287' Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 22 through 35 Processing helix chain 'H' and resid 45 through 55 Processing helix chain 'H' and resid 63 through 76 Processing helix chain 'H' and resid 93 through 105 Processing helix chain 'H' and resid 107 through 115 Processing helix chain 'H' and resid 132 through 143 Processing helix chain 'H' and resid 161 through 169 Processing helix chain 'H' and resid 180 through 182 No H-bonds generated for 'chain 'H' and resid 180 through 182' Processing helix chain 'H' and resid 210 through 221 removed outlier: 4.105A pdb=" N ASN H 213 " --> pdb=" O ILE H 210 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN H 214 " --> pdb=" O GLY H 211 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA H 221 " --> pdb=" O CYS H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 251 No H-bonds generated for 'chain 'H' and resid 248 through 251' Processing helix chain 'H' and resid 278 through 280 No H-bonds generated for 'chain 'H' and resid 278 through 280' Processing helix chain 'H' and resid 294 through 303 removed outlier: 3.701A pdb=" N ASP H 298 " --> pdb=" O SER H 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 54 through 71 removed outlier: 3.947A pdb=" N ARG C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 95 Processing helix chain 'C' and resid 127 through 145 Processing helix chain 'C' and resid 147 through 158 removed outlier: 4.688A pdb=" N LEU C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLU C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N HIS C 158 " --> pdb=" O GLN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 183 removed outlier: 4.124A pdb=" N ARG C 183 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 208 Processing helix chain 'C' and resid 219 through 228 removed outlier: 3.842A pdb=" N ILE C 222 " --> pdb=" O ASP C 219 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N PHE C 223 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET C 226 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER C 227 " --> pdb=" O ALA C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 297 through 299 No H-bonds generated for 'chain 'C' and resid 297 through 299' Processing helix chain 'C' and resid 301 through 303 No H-bonds generated for 'chain 'C' and resid 301 through 303' Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 333 through 343 removed outlier: 3.950A pdb=" N ILE C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N TYR C 337 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 343 " --> pdb=" O MET C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 348 No H-bonds generated for 'chain 'C' and resid 346 through 348' Processing helix chain 'F' and resid 192 through 195 removed outlier: 3.870A pdb=" N PHE F 195 " --> pdb=" O LEU F 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 192 through 195' Processing helix chain 'F' and resid 205 through 215 Processing helix chain 'F' and resid 222 through 238 removed outlier: 3.773A pdb=" N CYS F 226 " --> pdb=" O SER F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 266 removed outlier: 4.653A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS F 257 " --> pdb=" O VAL F 253 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 271 through 285 Processing helix chain 'F' and resid 293 through 324 removed outlier: 5.619A pdb=" N ALA F 315 " --> pdb=" O LYS F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 352 removed outlier: 3.574A pdb=" N GLU F 352 " --> pdb=" O GLU F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 378 removed outlier: 3.978A pdb=" N HIS F 378 " --> pdb=" O SER F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 394 removed outlier: 4.055A pdb=" N SER F 392 " --> pdb=" O ILE F 388 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR F 393 " --> pdb=" O PRO F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 429 Processing helix chain 'F' and resid 440 through 442 No H-bonds generated for 'chain 'F' and resid 440 through 442' Processing helix chain 'F' and resid 460 through 462 No H-bonds generated for 'chain 'F' and resid 460 through 462' Processing helix chain 'F' and resid 509 through 519 removed outlier: 3.593A pdb=" N VAL F 512 " --> pdb=" O CYS F 509 " (cutoff:3.500A) Proline residue: F 513 - end of helix removed outlier: 3.626A pdb=" N LYS F 519 " --> pdb=" O LEU F 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 99 through 107 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 131 through 141 Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 269 through 277 Processing helix chain 'A' and resid 303 through 314 Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'I' and resid 36 through 45 removed outlier: 3.830A pdb=" N LEU I 40 " --> pdb=" O ILE I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 69 removed outlier: 4.141A pdb=" N MET I 69 " --> pdb=" O ALA I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 92 Processing helix chain 'I' and resid 94 through 96 No H-bonds generated for 'chain 'I' and resid 94 through 96' Processing helix chain 'I' and resid 115 through 123 Processing helix chain 'I' and resid 184 through 189 Processing helix chain 'I' and resid 209 through 217 Processing helix chain 'I' and resid 284 through 287 No H-bonds generated for 'chain 'I' and resid 284 through 287' Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'G' and resid 45 through 55 Processing helix chain 'G' and resid 63 through 76 Processing helix chain 'G' and resid 93 through 105 Processing helix chain 'G' and resid 107 through 115 Processing helix chain 'G' and resid 132 through 143 Processing helix chain 'G' and resid 161 through 169 Processing helix chain 'G' and resid 180 through 182 No H-bonds generated for 'chain 'G' and resid 180 through 182' Processing helix chain 'G' and resid 210 through 221 removed outlier: 4.108A pdb=" N ASN G 213 " --> pdb=" O ILE G 210 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN G 214 " --> pdb=" O GLY G 211 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA G 221 " --> pdb=" O CYS G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 251 No H-bonds generated for 'chain 'G' and resid 248 through 251' Processing helix chain 'G' and resid 278 through 280 No H-bonds generated for 'chain 'G' and resid 278 through 280' Processing helix chain 'G' and resid 294 through 303 removed outlier: 3.700A pdb=" N ASP G 298 " --> pdb=" O SER G 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 31 through 47 Processing helix chain 'D' and resid 54 through 71 removed outlier: 3.947A pdb=" N ARG D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 95 Processing helix chain 'D' and resid 127 through 145 Processing helix chain 'D' and resid 147 through 158 removed outlier: 4.690A pdb=" N LEU D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLU D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N HIS D 158 " --> pdb=" O GLN D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 183 removed outlier: 4.129A pdb=" N ARG D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 208 Processing helix chain 'D' and resid 219 through 228 removed outlier: 3.842A pdb=" N ILE D 222 " --> pdb=" O ASP D 219 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N PHE D 223 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET D 226 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER D 227 " --> pdb=" O ALA D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 297 through 299 No H-bonds generated for 'chain 'D' and resid 297 through 299' Processing helix chain 'D' and resid 301 through 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing helix chain 'D' and resid 318 through 320 No H-bonds generated for 'chain 'D' and resid 318 through 320' Processing helix chain 'D' and resid 333 through 343 removed outlier: 3.949A pdb=" N ILE D 336 " --> pdb=" O PRO D 333 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N TYR D 337 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 343 " --> pdb=" O MET D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 348 No H-bonds generated for 'chain 'D' and resid 346 through 348' Processing helix chain 'E' and resid 192 through 195 removed outlier: 3.871A pdb=" N PHE E 195 " --> pdb=" O LEU E 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 192 through 195' Processing helix chain 'E' and resid 205 through 215 Processing helix chain 'E' and resid 222 through 238 removed outlier: 3.774A pdb=" N CYS E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 266 removed outlier: 4.655A pdb=" N VAL E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS E 257 " --> pdb=" O VAL E 253 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 271 through 285 Processing helix chain 'E' and resid 293 through 324 removed outlier: 5.620A pdb=" N ALA E 315 " --> pdb=" O LYS E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 352 removed outlier: 3.574A pdb=" N GLU E 352 " --> pdb=" O GLU E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 378 removed outlier: 3.979A pdb=" N HIS E 378 " --> pdb=" O SER E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 394 removed outlier: 4.046A pdb=" N SER E 392 " --> pdb=" O ILE E 388 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR E 393 " --> pdb=" O PRO E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 429 Processing helix chain 'E' and resid 440 through 442 No H-bonds generated for 'chain 'E' and resid 440 through 442' Processing helix chain 'E' and resid 460 through 462 No H-bonds generated for 'chain 'E' and resid 460 through 462' Processing helix chain 'E' and resid 509 through 519 removed outlier: 3.594A pdb=" N VAL E 512 " --> pdb=" O CYS E 509 " (cutoff:3.500A) Proline residue: E 513 - end of helix removed outlier: 3.626A pdb=" N LYS E 519 " --> pdb=" O LEU E 516 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 149 through 152 removed outlier: 6.815A pdb=" N GLU B 90 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU B 47 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N PHE B 92 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 119 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL B 93 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ARG B 121 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N CYS B 95 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE B 123 " --> pdb=" O CYS B 95 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 155 through 157 Processing sheet with id= C, first strand: chain 'B' and resid 244 through 246 removed outlier: 7.454A pdb=" N GLN B 286 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR B 182 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N HIS B 288 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE B 184 " --> pdb=" O HIS B 288 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N HIS B 290 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LYS B 186 " --> pdb=" O HIS B 290 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N THR B 292 " --> pdb=" O LYS B 186 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 203 through 206 Processing sheet with id= E, first strand: chain 'B' and resid 335 through 337 Processing sheet with id= F, first strand: chain 'B' and resid 373 through 375 removed outlier: 3.535A pdb=" N ILE B 408 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP B 392 " --> pdb=" O ILE B 408 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 429 through 431 removed outlier: 6.252A pdb=" N SER B 447 " --> pdb=" O VAL B 430 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'J' and resid 100 through 105 removed outlier: 3.624A pdb=" N LEU J 102 " --> pdb=" O GLN J 4 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE J 52 " --> pdb=" O ALA J 5 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL J 7 " --> pdb=" O ILE J 52 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N VAL J 76 " --> pdb=" O VAL J 53 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'J' and resid 128 through 133 Processing sheet with id= J, first strand: chain 'J' and resid 193 through 196 removed outlier: 3.668A pdb=" N ALA J 171 " --> pdb=" O PHE J 157 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASP J 161 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU J 167 " --> pdb=" O ASP J 161 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 124 through 127 removed outlier: 6.639A pdb=" N SER H 149 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N THR H 127 " --> pdb=" O SER H 149 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TYR H 151 " --> pdb=" O THR H 127 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 192 through 196 removed outlier: 7.329A pdb=" N VAL H 195 " --> pdb=" O PRO H 225 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TYR H 227 " --> pdb=" O VAL H 195 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'H' and resid 206 through 209 removed outlier: 4.089A pdb=" N ASN H 208 " --> pdb=" O ASP H 274 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 284 through 286 Processing sheet with id= O, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.642A pdb=" N HIS C 188 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N THR C 167 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE C 190 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET C 217 " --> pdb=" O VAL C 191 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 232 through 234 removed outlier: 6.940A pdb=" N LEU C 323 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 326 " --> pdb=" O GLY C 329 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 245 through 248 removed outlier: 3.795A pdb=" N ALA C 247 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP C 314 " --> pdb=" O ALA C 247 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 332 through 336 removed outlier: 6.524A pdb=" N ARG F 357 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL F 335 " --> pdb=" O ARG F 357 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL F 359 " --> pdb=" O VAL F 335 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL F 360 " --> pdb=" O PRO F 382 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N SER F 384 " --> pdb=" O VAL F 360 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASP F 362 " --> pdb=" O SER F 384 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU F 386 " --> pdb=" O ASP F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'F' and resid 400 through 404 removed outlier: 7.756A pdb=" N LEU F 403 " --> pdb=" O PRO F 433 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU F 435 " --> pdb=" O LEU F 403 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU F 499 " --> pdb=" O VAL F 436 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR F 502 " --> pdb=" O GLY F 505 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 405 through 408 removed outlier: 6.665A pdb=" N MET F 415 " --> pdb=" O HIS F 406 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 149 through 152 removed outlier: 6.814A pdb=" N GLU A 90 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU A 47 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N PHE A 92 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL A 119 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL A 93 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ARG A 121 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N CYS A 95 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE A 123 " --> pdb=" O CYS A 95 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 155 through 157 Processing sheet with id= W, first strand: chain 'A' and resid 244 through 246 removed outlier: 7.454A pdb=" N GLN A 286 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR A 182 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N HIS A 288 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE A 184 " --> pdb=" O HIS A 288 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N HIS A 290 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LYS A 186 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N THR A 292 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 203 through 206 Processing sheet with id= Y, first strand: chain 'A' and resid 335 through 337 Processing sheet with id= Z, first strand: chain 'A' and resid 373 through 375 removed outlier: 3.539A pdb=" N ILE A 408 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP A 392 " --> pdb=" O ILE A 408 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 429 through 431 removed outlier: 6.235A pdb=" N SER A 447 " --> pdb=" O VAL A 430 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'I' and resid 100 through 105 removed outlier: 3.625A pdb=" N LEU I 102 " --> pdb=" O GLN I 4 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE I 52 " --> pdb=" O ALA I 5 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL I 7 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL I 76 " --> pdb=" O VAL I 53 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'I' and resid 128 through 131 Processing sheet with id= AD, first strand: chain 'I' and resid 193 through 196 removed outlier: 3.648A pdb=" N ALA I 171 " --> pdb=" O PHE I 157 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP I 161 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU I 167 " --> pdb=" O ASP I 161 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 124 through 127 removed outlier: 6.638A pdb=" N SER G 149 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N THR G 127 " --> pdb=" O SER G 149 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TYR G 151 " --> pdb=" O THR G 127 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 192 through 195 removed outlier: 7.332A pdb=" N VAL G 195 " --> pdb=" O PRO G 225 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR G 227 " --> pdb=" O VAL G 195 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'G' and resid 206 through 209 removed outlier: 4.088A pdb=" N ASN G 208 " --> pdb=" O ASP G 274 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 284 through 286 Processing sheet with id= AI, first strand: chain 'D' and resid 164 through 168 removed outlier: 6.640A pdb=" N HIS D 188 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR D 167 " --> pdb=" O HIS D 188 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE D 190 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET D 217 " --> pdb=" O VAL D 191 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'D' and resid 232 through 234 removed outlier: 6.940A pdb=" N LEU D 323 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER D 326 " --> pdb=" O GLY D 329 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'D' and resid 245 through 248 removed outlier: 3.792A pdb=" N ALA D 247 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP D 314 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'E' and resid 332 through 336 removed outlier: 6.524A pdb=" N ARG E 357 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL E 335 " --> pdb=" O ARG E 357 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL E 359 " --> pdb=" O VAL E 335 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL E 360 " --> pdb=" O PRO E 382 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER E 384 " --> pdb=" O VAL E 360 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ASP E 362 " --> pdb=" O SER E 384 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU E 386 " --> pdb=" O ASP E 362 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'E' and resid 400 through 404 removed outlier: 7.758A pdb=" N LEU E 403 " --> pdb=" O PRO E 433 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU E 435 " --> pdb=" O LEU E 403 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU E 499 " --> pdb=" O VAL E 436 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR E 502 " --> pdb=" O GLY E 505 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'E' and resid 405 through 408 removed outlier: 6.665A pdb=" N MET E 415 " --> pdb=" O HIS E 406 " (cutoff:3.500A) 774 hydrogen bonds defined for protein. 2124 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.07 Time building geometry restraints manager: 10.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.41: 9872 1.41 - 1.65: 14681 1.65 - 1.88: 190 1.88 - 2.11: 0 2.11 - 2.35: 1 Bond restraints: 24744 Sorted by residual: bond pdb=" C ILE J 267 " pdb=" N THR J 272 " ideal model delta sigma weight residual 1.329 2.346 -1.017 1.44e-02 4.82e+03 4.99e+03 bond pdb=" C16BC7B C 401 " pdb=" N08BC7B C 401 " ideal model delta sigma weight residual 1.341 1.442 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C15AC7B C 401 " pdb=" N07AC7B C 401 " ideal model delta sigma weight residual 1.341 1.441 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C16AC7B C 401 " pdb=" N08AC7B C 401 " ideal model delta sigma weight residual 1.341 1.441 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C15BC7B C 401 " pdb=" N07BC7B C 401 " ideal model delta sigma weight residual 1.341 1.439 -0.098 2.00e-02 2.50e+03 2.40e+01 ... (remaining 24739 not shown) Histogram of bond angle deviations from ideal: 96.25 - 103.80: 336 103.80 - 111.35: 10303 111.35 - 118.90: 9790 118.90 - 126.45: 12884 126.45 - 134.00: 318 Bond angle restraints: 33631 Sorted by residual: angle pdb=" C ILE J 267 " pdb=" N THR J 272 " pdb=" CA THR J 272 " ideal model delta sigma weight residual 122.64 96.25 26.39 1.70e+00 3.46e-01 2.41e+02 angle pdb=" O ILE J 267 " pdb=" C ILE J 267 " pdb=" N THR J 272 " ideal model delta sigma weight residual 122.76 114.16 8.60 1.47e+00 4.63e-01 3.42e+01 angle pdb=" C LEU E 387 " pdb=" N ILE E 388 " pdb=" CA ILE E 388 " ideal model delta sigma weight residual 120.33 124.77 -4.44 8.00e-01 1.56e+00 3.08e+01 angle pdb=" C LEU F 387 " pdb=" N ILE F 388 " pdb=" CA ILE F 388 " ideal model delta sigma weight residual 120.33 124.73 -4.40 8.00e-01 1.56e+00 3.02e+01 angle pdb=" C THR A 209 " pdb=" N ASN A 210 " pdb=" CA ASN A 210 " ideal model delta sigma weight residual 122.46 129.43 -6.97 1.41e+00 5.03e-01 2.45e+01 ... (remaining 33626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 14837 34.00 - 68.00: 58 68.00 - 102.00: 14 102.00 - 136.00: 4 136.00 - 170.00: 2 Dihedral angle restraints: 14915 sinusoidal: 5554 harmonic: 9361 Sorted by residual: dihedral pdb=" CA GLN G 156 " pdb=" C GLN G 156 " pdb=" N PRO G 157 " pdb=" CA PRO G 157 " ideal model delta harmonic sigma weight residual 180.00 140.39 39.61 0 5.00e+00 4.00e-02 6.27e+01 dihedral pdb=" CA GLN H 156 " pdb=" C GLN H 156 " pdb=" N PRO H 157 " pdb=" CA PRO H 157 " ideal model delta harmonic sigma weight residual 180.00 140.49 39.51 0 5.00e+00 4.00e-02 6.24e+01 dihedral pdb=" CA ALA C 195 " pdb=" C ALA C 195 " pdb=" N PRO C 196 " pdb=" CA PRO C 196 " ideal model delta harmonic sigma weight residual 180.00 142.84 37.16 0 5.00e+00 4.00e-02 5.52e+01 ... (remaining 14912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.018: 4003 1.018 - 2.036: 0 2.036 - 3.054: 0 3.054 - 4.072: 0 4.072 - 5.090: 4 Chirality restraints: 4007 Sorted by residual: chirality pdb=" C09AC7B C 401 " pdb=" C13AC7B C 401 " pdb=" C14AC7B C 401 " pdb=" N07AC7B C 401 " both_signs ideal model delta sigma weight residual False 2.47 -2.62 5.09 2.00e-01 2.50e+01 6.48e+02 chirality pdb=" C09BC7B C 401 " pdb=" C13BC7B C 401 " pdb=" C14BC7B C 401 " pdb=" N07BC7B C 401 " both_signs ideal model delta sigma weight residual False 2.47 -2.62 5.09 2.00e-01 2.50e+01 6.48e+02 chirality pdb=" C10BC7B C 401 " pdb=" C11BC7B C 401 " pdb=" C12BC7B C 401 " pdb=" N08BC7B C 401 " both_signs ideal model delta sigma weight residual False 2.47 -2.50 4.97 2.00e-01 2.50e+01 6.18e+02 ... (remaining 4004 not shown) Planarity restraints: 4297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE J 267 " -0.079 2.00e-02 2.50e+03 1.31e-01 1.72e+02 pdb=" C ILE J 267 " 0.225 2.00e-02 2.50e+03 pdb=" O ILE J 267 " -0.100 2.00e-02 2.50e+03 pdb=" N THR J 272 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN H 156 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO H 157 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO H 157 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 157 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN G 156 " -0.042 5.00e-02 4.00e+02 6.41e-02 6.58e+00 pdb=" N PRO G 157 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO G 157 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 157 " -0.036 5.00e-02 4.00e+02 ... (remaining 4294 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.15: 3 2.15 - 2.84: 7561 2.84 - 3.53: 32116 3.53 - 4.21: 57330 4.21 - 4.90: 97561 Nonbonded interactions: 194571 Sorted by model distance: nonbonded pdb=" CD2 PHE I 266 " pdb=" CG2 THR I 272 " model vdw 1.467 3.760 nonbonded pdb=" CE2 PHE I 266 " pdb=" CG2 THR I 272 " model vdw 1.474 3.760 nonbonded pdb=" O ILE I 267 " pdb=" CB THR I 272 " model vdw 2.063 3.470 nonbonded pdb=" CE2 PHE I 266 " pdb=" OG1 THR I 272 " model vdw 2.273 3.340 nonbonded pdb=" CE2 PHE I 266 " pdb=" CB THR I 272 " model vdw 2.292 3.770 ... (remaining 194566 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 8 through 351) selection = chain 'D' } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 166 through 521 or (resid 522 and (name N or name CA or na \ me C or name O )))) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 122 5.16 5 Cl 4 4.86 5 C 15461 2.51 5 N 4238 2.21 5 O 4470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.550 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: 0.020 Extract box with map and model: 16.720 Check model and map are aligned: 0.390 Process input model: 60.400 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.210 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0156 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 : 0.008 1.017 24744 Z= 0.427 Angle : 0.879 26.386 33631 Z= 0.490 Chirality : 0.167 5.090 4007 Planarity : 0.007 0.131 4297 Dihedral : 9.838 170.000 8825 Min Nonbonded Distance : 1.467 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -3.63 (0.12), residues: 3150 helix: -2.59 (0.10), residues: 1204 sheet: -2.05 (0.22), residues: 410 loop : -2.29 (0.14), residues: 1536 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 212 time to evaluate : 2.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 217 average time/residue: 1.3908 time to fit residues: 350.4297 Evaluate side-chains 140 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 2.645 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.2783 time to fit residues: 4.4758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 0.0000 chunk 239 optimal weight: 50.0000 chunk 132 optimal weight: 2.9990 chunk 81 optimal weight: 50.0000 chunk 161 optimal weight: 40.0000 chunk 127 optimal weight: 4.9990 chunk 247 optimal weight: 50.0000 chunk 95 optimal weight: 40.0000 chunk 150 optimal weight: 0.8980 chunk 184 optimal weight: 20.0000 chunk 286 optimal weight: 40.0000 overall best weight: 5.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 160 ASN B 248 HIS B 290 HIS B 359 ASN B 376 ASN J 218 ASN H 213 ASN H 243 GLN ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 GLN ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 GLN A 89 GLN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 218 ASN ** G 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 ASN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS ** E 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** E 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 347 GLN ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0275 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.124 24744 Z= 0.473 Angle : 1.001 20.130 33631 Z= 0.512 Chirality : 0.056 0.391 4007 Planarity : 0.008 0.116 4297 Dihedral : 7.687 160.068 3451 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.90 % Favored : 94.00 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 4.29 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.13), residues: 3152 helix: -1.38 (0.13), residues: 1192 sheet: -2.13 (0.25), residues: 381 loop : -2.01 (0.14), residues: 1579 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 146 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 30 residues processed: 189 average time/residue: 1.2510 time to fit residues: 278.8491 Evaluate side-chains 159 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 129 time to evaluate : 2.731 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 21 residues processed: 9 average time/residue: 1.2301 time to fit residues: 16.9510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 159 optimal weight: 40.0000 chunk 89 optimal weight: 6.9990 chunk 238 optimal weight: 30.0000 chunk 195 optimal weight: 40.0000 chunk 79 optimal weight: 20.0000 chunk 287 optimal weight: 50.0000 chunk 310 optimal weight: 1.9990 chunk 256 optimal weight: 0.6980 chunk 285 optimal weight: 50.0000 chunk 98 optimal weight: 30.0000 chunk 230 optimal weight: 50.0000 overall best weight: 11.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 222 GLN C 162 ASN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN ** F 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 GLN ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 HIS ** F 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 HIS A 216 GLN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN A 359 ASN A 376 ASN ** G 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 ASN ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN ** E 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS E 378 HIS E 406 HIS E 422 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0590 moved from start: 0.7542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.190 24744 Z= 0.860 Angle : 1.562 24.254 33631 Z= 0.813 Chirality : 0.075 0.504 4007 Planarity : 0.013 0.180 4297 Dihedral : 10.513 141.284 3451 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 40.21 Ramachandran Plot: Outliers : 0.67 % Allowed : 10.31 % Favored : 89.02 % Rotamer Outliers : 6.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 6.43 % Twisted General : 1.55 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.13), residues: 3152 helix: -1.59 (0.14), residues: 1125 sheet: -2.40 (0.27), residues: 328 loop : -2.48 (0.14), residues: 1699 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 141 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 157 outliers final: 90 residues processed: 267 average time/residue: 1.1643 time to fit residues: 371.3924 Evaluate side-chains 216 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 126 time to evaluate : 2.390 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 74 residues processed: 16 average time/residue: 1.2736 time to fit residues: 27.8166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 284 optimal weight: 6.9990 chunk 216 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 chunk 31 optimal weight: 30.0000 chunk 137 optimal weight: 1.9990 chunk 193 optimal weight: 30.0000 chunk 288 optimal weight: 3.9990 chunk 305 optimal weight: 8.9990 chunk 150 optimal weight: 0.6980 chunk 273 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS ** F 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 HIS ** G 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 HIS E 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0460 moved from start: 0.7193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 24744 Z= 0.243 Angle : 0.765 13.562 33631 Z= 0.392 Chirality : 0.049 0.339 4007 Planarity : 0.006 0.107 4297 Dihedral : 8.163 162.414 3451 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 4.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.14), residues: 3152 helix: -0.80 (0.15), residues: 1147 sheet: -2.01 (0.26), residues: 360 loop : -2.24 (0.14), residues: 1645 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 136 time to evaluate : 2.815 Fit side-chains revert: symmetry clash outliers start: 126 outliers final: 76 residues processed: 248 average time/residue: 1.1141 time to fit residues: 333.4434 Evaluate side-chains 200 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 124 time to evaluate : 2.662 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 69 residues processed: 8 average time/residue: 0.9333 time to fit residues: 12.9953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 254 optimal weight: 0.4980 chunk 173 optimal weight: 50.0000 chunk 4 optimal weight: 50.0000 chunk 227 optimal weight: 40.0000 chunk 126 optimal weight: 0.9980 chunk 260 optimal weight: 1.9990 chunk 211 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 155 optimal weight: 0.7980 chunk 274 optimal weight: 0.0000 chunk 77 optimal weight: 30.0000 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 477 GLN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 HIS E 265 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0415 moved from start: 0.7108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 24744 Z= 0.170 Angle : 0.635 11.350 33631 Z= 0.322 Chirality : 0.045 0.269 4007 Planarity : 0.005 0.072 4297 Dihedral : 7.192 165.154 3451 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 4.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.07 % 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: -1.95 (0.15), residues: 3152 helix: -0.25 (0.15), residues: 1170 sheet: -1.68 (0.26), residues: 364 loop : -2.01 (0.15), residues: 1618 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 132 time to evaluate : 2.580 Fit side-chains revert: symmetry clash outliers start: 122 outliers final: 83 residues processed: 233 average time/residue: 1.0514 time to fit residues: 296.3419 Evaluate side-chains 209 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 126 time to evaluate : 2.811 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 72 residues processed: 11 average time/residue: 1.0380 time to fit residues: 17.7084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 102 optimal weight: 40.0000 chunk 275 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 179 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 305 optimal weight: 8.9990 chunk 253 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 25 optimal weight: 50.0000 chunk 101 optimal weight: 50.0000 chunk 160 optimal weight: 50.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN ** G 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0509 moved from start: 0.7966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.108 24744 Z= 0.374 Angle : 0.874 16.176 33631 Z= 0.445 Chirality : 0.053 0.470 4007 Planarity : 0.007 0.090 4297 Dihedral : 8.084 162.364 3451 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 23.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer Outliers : 5.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.15), residues: 3152 helix: -0.23 (0.16), residues: 1132 sheet: -2.06 (0.26), residues: 365 loop : -1.99 (0.15), residues: 1655 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 139 time to evaluate : 2.758 Fit side-chains revert: symmetry clash outliers start: 140 outliers final: 103 residues processed: 260 average time/residue: 1.1207 time to fit residues: 357.1202 Evaluate side-chains 233 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 130 time to evaluate : 2.700 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 92 residues processed: 11 average time/residue: 0.9899 time to fit residues: 17.2430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 294 optimal weight: 50.0000 chunk 34 optimal weight: 40.0000 chunk 174 optimal weight: 3.9990 chunk 223 optimal weight: 9.9990 chunk 172 optimal weight: 0.8980 chunk 257 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 304 optimal weight: 0.9990 chunk 190 optimal weight: 50.0000 chunk 185 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0446 moved from start: 0.7836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 24744 Z= 0.169 Angle : 0.633 10.447 33631 Z= 0.320 Chirality : 0.046 0.287 4007 Planarity : 0.005 0.095 4297 Dihedral : 7.183 169.428 3451 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 5.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.07 % 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: -1.56 (0.15), residues: 3152 helix: 0.17 (0.16), residues: 1142 sheet: -1.83 (0.26), residues: 369 loop : -1.73 (0.15), residues: 1641 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 129 time to evaluate : 2.743 Fit side-chains revert: symmetry clash outliers start: 130 outliers final: 103 residues processed: 243 average time/residue: 1.0618 time to fit residues: 311.4454 Evaluate side-chains 225 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 122 time to evaluate : 2.424 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 93 residues processed: 10 average time/residue: 1.0189 time to fit residues: 15.8133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 188 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 chunk 181 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 207 optimal weight: 50.0000 chunk 150 optimal weight: 0.8980 chunk 28 optimal weight: 40.0000 chunk 239 optimal weight: 9.9990 chunk 277 optimal weight: 0.8980 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0525 moved from start: 0.8438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 24744 Z= 0.299 Angle : 0.790 15.767 33631 Z= 0.400 Chirality : 0.050 0.258 4007 Planarity : 0.007 0.101 4297 Dihedral : 7.725 167.170 3451 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer Outliers : 4.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.10 % 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: -1.68 (0.15), residues: 3152 helix: 0.08 (0.16), residues: 1130 sheet: -1.97 (0.26), residues: 360 loop : -1.78 (0.15), residues: 1662 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 128 time to evaluate : 2.606 Fit side-chains revert: symmetry clash outliers start: 125 outliers final: 103 residues processed: 239 average time/residue: 1.1178 time to fit residues: 320.3337 Evaluate side-chains 229 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 126 time to evaluate : 2.690 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 92 residues processed: 11 average time/residue: 1.1896 time to fit residues: 20.2099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 291 optimal weight: 5.9990 chunk 266 optimal weight: 0.1980 chunk 283 optimal weight: 10.0000 chunk 170 optimal weight: 0.7980 chunk 123 optimal weight: 0.2980 chunk 222 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 256 optimal weight: 0.0470 chunk 268 optimal weight: 0.3980 chunk 282 optimal weight: 0.9980 chunk 186 optimal weight: 10.0000 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 ASN ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 270 HIS D 132 ASN D 138 ASN D 252 HIS ** D 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0444 moved from start: 0.8207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 24744 Z= 0.152 Angle : 0.614 14.352 33631 Z= 0.309 Chirality : 0.045 0.264 4007 Planarity : 0.005 0.094 4297 Dihedral : 6.933 172.032 3451 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 4.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.03 % 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: -1.26 (0.15), residues: 3152 helix: 0.44 (0.16), residues: 1151 sheet: -1.77 (0.26), residues: 364 loop : -1.56 (0.15), residues: 1637 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 119 time to evaluate : 2.409 Fit side-chains revert: symmetry clash outliers start: 113 outliers final: 98 residues processed: 222 average time/residue: 1.0987 time to fit residues: 295.8295 Evaluate side-chains 211 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 113 time to evaluate : 2.558 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 92 residues processed: 6 average time/residue: 1.4420 time to fit residues: 13.9250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 300 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 208 optimal weight: 20.0000 chunk 314 optimal weight: 0.7980 chunk 289 optimal weight: 8.9990 chunk 250 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 199 optimal weight: 50.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 ASN ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 ASN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0524 moved from start: 0.8685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 24744 Z= 0.273 Angle : 0.742 12.194 33631 Z= 0.376 Chirality : 0.048 0.252 4007 Planarity : 0.006 0.090 4297 Dihedral : 7.450 172.009 3451 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer Outliers : 4.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.10 % 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: -1.41 (0.15), residues: 3152 helix: 0.32 (0.16), residues: 1136 sheet: -1.88 (0.27), residues: 354 loop : -1.64 (0.15), residues: 1662 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 122 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 98 residues processed: 219 average time/residue: 1.0809 time to fit residues: 286.9248 Evaluate side-chains 217 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 119 time to evaluate : 2.570 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 89 residues processed: 9 average time/residue: 1.0040 time to fit residues: 14.6078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 267 optimal weight: 0.9980 chunk 76 optimal weight: 0.0770 chunk 231 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 69 optimal weight: 50.0000 chunk 251 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 257 optimal weight: 0.9980 chunk 31 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 220 optimal weight: 40.0000 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 HIS ** J 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 ASN ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN D 138 ASN ** D 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5441 r_free = 0.5441 target = 0.313423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5370 r_free = 0.5370 target = 0.295798 restraints weight = 55689.041| |-----------------------------------------------------------------------------| r_work (start): 0.5339 rms_B_bonded: 4.47 r_work (final): 0.5339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5441 r_free = 0.5441 target_work(ls_wunit_k1) = 0.313 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5441 r_free = 0.5441 target_work(ls_wunit_k1) = 0.313 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.5441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1419 moved from start: 0.8542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 24744 Z= 0.155 Angle : 0.607 10.762 33631 Z= 0.305 Chirality : 0.045 0.245 4007 Planarity : 0.005 0.093 4297 Dihedral : 6.933 178.398 3451 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 3.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.03 % 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: -1.06 (0.15), residues: 3152 helix: 0.62 (0.16), residues: 1144 sheet: -1.74 (0.26), residues: 362 loop : -1.43 (0.15), residues: 1646 =============================================================================== Job complete usr+sys time: 6840.93 seconds wall clock time: 124 minutes 49.53 seconds (7489.53 seconds total)