Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 04:17:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caj_7442/04_2023/6caj_7442_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caj_7442/04_2023/6caj_7442.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_7442/04_2023/6caj_7442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caj_7442/04_2023/6caj_7442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caj_7442/04_2023/6caj_7442_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caj_7442/04_2023/6caj_7442_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= 0.055 sd= 1.469 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians 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. 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 12.90, per 1000 atoms: 0.53 Number of scatterers: 24295 At special positions: 0 Unit cell: (134.918, 171.79, 118.996, 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: 9.59 Conformation dependent library (CDL) restraints added in 3.9 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: 2.66 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: 8.06 Time building geometry restraints manager: 10.28 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.260 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: 21.310 Check model and map are aligned: 0.400 Set scattering table: 0.220 Process input model: 60.760 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1591 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 834 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 828 time to evaluate : 2.808 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 832 average time/residue: 1.3558 time to fit residues: 1293.5938 Evaluate side-chains 425 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 423 time to evaluate : 2.817 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.4128 time to fit residues: 5.2227 ------------------------------------------------------------------------------- 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: 0.1980 chunk 239 optimal weight: 0.0980 chunk 132 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 247 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 286 optimal weight: 4.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 GLN B 101 GLN B 255 GLN B 258 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS B 371 ASN B 409 HIS B 410 GLN J 218 ASN H 213 ASN H 243 GLN H 244 GLN C 150 ASN C 160 HIS C 206 ASN C 252 HIS C 286 HIS F 275 ASN F 347 GLN F 406 HIS F 422 GLN F 430 HIS A 63 GLN A 101 GLN A 255 GLN A 258 GLN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS A 371 ASN A 409 HIS A 410 GLN I 203 HIS I 218 ASN G 213 ASN G 243 GLN G 244 GLN G 270 HIS D 150 ASN D 160 HIS D 206 ASN D 252 HIS D 286 HIS E 275 ASN E 347 GLN E 406 HIS E 422 GLN E 430 HIS Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1514 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 24744 Z= 0.225 Angle : 0.616 12.452 33631 Z= 0.308 Chirality : 0.045 0.166 4007 Planarity : 0.005 0.058 4297 Dihedral : 6.317 167.730 3451 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 4.69 % 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: -1.88 (0.14), residues: 3152 helix: -0.59 (0.14), residues: 1200 sheet: -1.79 (0.22), residues: 469 loop : -1.54 (0.15), residues: 1483 *********************** 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 585 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 466 time to evaluate : 2.947 Fit side-chains revert: symmetry clash outliers start: 119 outliers final: 33 residues processed: 542 average time/residue: 1.2882 time to fit residues: 809.2630 Evaluate side-chains 397 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 364 time to evaluate : 2.929 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 23 residues processed: 10 average time/residue: 0.5698 time to fit residues: 11.5412 ------------------------------------------------------------------------------- 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: 0.2980 chunk 89 optimal weight: 0.9990 chunk 238 optimal weight: 0.6980 chunk 195 optimal weight: 0.0980 chunk 79 optimal weight: 0.2980 chunk 287 optimal weight: 2.9990 chunk 310 optimal weight: 0.4980 chunk 256 optimal weight: 1.9990 chunk 285 optimal weight: 0.6980 chunk 98 optimal weight: 0.0040 chunk 230 optimal weight: 4.9990 overall best weight: 0.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN B 216 GLN B 288 HIS ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS H 244 GLN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN F 254 ASN F 309 GLN ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS G 244 GLN D 44 GLN D 206 ASN E 254 ASN E 309 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1505 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 24744 Z= 0.137 Angle : 0.530 9.676 33631 Z= 0.263 Chirality : 0.043 0.232 4007 Planarity : 0.004 0.053 4297 Dihedral : 6.044 168.152 3451 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 4.96 % 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: -1.10 (0.14), residues: 3152 helix: 0.17 (0.15), residues: 1206 sheet: -1.36 (0.24), residues: 439 loop : -1.23 (0.15), residues: 1507 *********************** 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 494 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 368 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 126 outliers final: 50 residues processed: 443 average time/residue: 1.3036 time to fit residues: 671.7174 Evaluate side-chains 380 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 330 time to evaluate : 3.126 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 35 residues processed: 15 average time/residue: 0.6579 time to fit residues: 16.9465 ------------------------------------------------------------------------------- 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: 1.9990 chunk 216 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 193 optimal weight: 0.9980 chunk 288 optimal weight: 2.9990 chunk 305 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 273 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 218 ASN C 158 HIS ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN F 431 ASN A 101 GLN A 263 ASN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 218 ASN D 158 HIS E 254 ASN E 431 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1450 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 24744 Z= 0.267 Angle : 0.605 10.641 33631 Z= 0.304 Chirality : 0.046 0.213 4007 Planarity : 0.005 0.051 4297 Dihedral : 6.383 171.360 3451 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 6.07 % 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: -0.91 (0.15), residues: 3152 helix: 0.28 (0.15), residues: 1228 sheet: -1.30 (0.22), residues: 485 loop : -1.04 (0.16), residues: 1439 *********************** 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 504 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 350 time to evaluate : 2.914 Fit side-chains revert: symmetry clash outliers start: 154 outliers final: 68 residues processed: 458 average time/residue: 1.3672 time to fit residues: 721.0543 Evaluate side-chains 372 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 304 time to evaluate : 2.881 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 57 residues processed: 15 average time/residue: 0.6279 time to fit residues: 16.2669 ------------------------------------------------------------------------------- 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: 2.9990 chunk 173 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 227 optimal weight: 9.9990 chunk 126 optimal weight: 0.5980 chunk 260 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 274 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 GLN ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 223 ASN C 138 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 431 ASN F 448 GLN A 255 GLN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 ASN D 138 ASN E 254 ASN E 431 ASN E 448 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1420 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 24744 Z= 0.280 Angle : 0.621 10.459 33631 Z= 0.310 Chirality : 0.046 0.214 4007 Planarity : 0.005 0.054 4297 Dihedral : 6.471 171.370 3451 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 5.36 % 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: -0.68 (0.15), residues: 3152 helix: 0.46 (0.15), residues: 1232 sheet: -1.18 (0.23), residues: 481 loop : -0.89 (0.16), residues: 1439 *********************** 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 458 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 322 time to evaluate : 3.255 Fit side-chains revert: symmetry clash outliers start: 136 outliers final: 66 residues processed: 426 average time/residue: 1.4117 time to fit residues: 695.4710 Evaluate side-chains 363 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 297 time to evaluate : 3.020 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 55 residues processed: 15 average time/residue: 0.4175 time to fit residues: 13.4760 ------------------------------------------------------------------------------- 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: 0.7980 chunk 275 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 305 optimal weight: 1.9990 chunk 253 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 GLN ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 223 ASN C 138 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 431 ASN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 ASN D 150 ASN ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1415 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 24744 Z= 0.228 Angle : 0.584 10.151 33631 Z= 0.291 Chirality : 0.044 0.211 4007 Planarity : 0.004 0.053 4297 Dihedral : 6.321 170.244 3451 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 4.37 % 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: -0.36 (0.15), residues: 3152 helix: 0.73 (0.15), residues: 1218 sheet: -1.09 (0.22), residues: 501 loop : -0.67 (0.17), residues: 1433 *********************** 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 419 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 308 time to evaluate : 2.882 Fit side-chains revert: symmetry clash outliers start: 111 outliers final: 69 residues processed: 396 average time/residue: 1.4661 time to fit residues: 664.2189 Evaluate side-chains 350 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 281 time to evaluate : 2.909 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 59 residues processed: 14 average time/residue: 0.3054 time to fit residues: 11.1070 ------------------------------------------------------------------------------- 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: 4.9990 chunk 34 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 223 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 257 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 chunk 304 optimal weight: 0.7980 chunk 190 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 190 HIS ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 GLN F 431 ASN A 255 GLN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 HIS ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN E 431 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1390 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.066 24744 Z= 0.385 Angle : 0.680 10.815 33631 Z= 0.343 Chirality : 0.048 0.209 4007 Planarity : 0.005 0.064 4297 Dihedral : 6.757 174.186 3451 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer Outliers : 4.81 % 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: -0.58 (0.15), residues: 3152 helix: 0.43 (0.15), residues: 1232 sheet: -1.04 (0.22), residues: 479 loop : -0.75 (0.17), residues: 1441 *********************** 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 432 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 310 time to evaluate : 3.194 Fit side-chains revert: symmetry clash outliers start: 122 outliers final: 75 residues processed: 399 average time/residue: 1.5044 time to fit residues: 691.4176 Evaluate side-chains 372 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 297 time to evaluate : 2.770 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 60 residues processed: 19 average time/residue: 0.4658 time to fit residues: 16.7220 ------------------------------------------------------------------------------- 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: 2.9990 chunk 121 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 193 optimal weight: 0.0970 chunk 207 optimal weight: 6.9990 chunk 150 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 239 optimal weight: 0.9990 chunk 277 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 223 ASN C 44 GLN C 150 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 GLN F 431 ASN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 ASN D 44 GLN ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1397 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 24744 Z= 0.224 Angle : 0.592 9.985 33631 Z= 0.298 Chirality : 0.044 0.201 4007 Planarity : 0.005 0.061 4297 Dihedral : 6.451 171.817 3451 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 4.14 % 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: -0.29 (0.15), residues: 3152 helix: 0.74 (0.15), residues: 1218 sheet: -0.99 (0.23), residues: 501 loop : -0.61 (0.17), residues: 1433 *********************** 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 412 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 307 time to evaluate : 3.211 Fit side-chains revert: symmetry clash outliers start: 105 outliers final: 73 residues processed: 390 average time/residue: 1.4049 time to fit residues: 632.0380 Evaluate side-chains 371 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 298 time to evaluate : 2.898 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 65 residues processed: 11 average time/residue: 0.4346 time to fit residues: 10.7743 ------------------------------------------------------------------------------- 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: 0.3980 chunk 266 optimal weight: 0.8980 chunk 283 optimal weight: 0.0070 chunk 170 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 222 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 256 optimal weight: 0.9980 chunk 268 optimal weight: 0.8980 chunk 282 optimal weight: 0.4980 chunk 186 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 431 ASN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN E 431 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1403 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 24744 Z= 0.193 Angle : 0.569 10.025 33631 Z= 0.286 Chirality : 0.043 0.209 4007 Planarity : 0.004 0.072 4297 Dihedral : 6.246 169.843 3451 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 3.51 % 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: -0.10 (0.15), residues: 3152 helix: 0.91 (0.15), residues: 1218 sheet: -0.89 (0.23), residues: 487 loop : -0.53 (0.17), residues: 1447 *********************** 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 406 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 317 time to evaluate : 3.254 Fit side-chains revert: symmetry clash outliers start: 89 outliers final: 66 residues processed: 391 average time/residue: 1.3901 time to fit residues: 631.3891 Evaluate side-chains 366 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 300 time to evaluate : 2.758 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 59 residues processed: 9 average time/residue: 0.2909 time to fit residues: 8.1889 ------------------------------------------------------------------------------- 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: 2.9990 chunk 183 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 314 optimal weight: 0.0870 chunk 289 optimal weight: 4.9990 chunk 250 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 193 optimal weight: 0.1980 chunk 153 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 overall best weight: 1.2564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 ASN ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 223 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 431 ASN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN G 223 ASN ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1388 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 24744 Z= 0.334 Angle : 0.662 10.282 33631 Z= 0.332 Chirality : 0.047 0.225 4007 Planarity : 0.005 0.072 4297 Dihedral : 6.629 172.541 3451 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 3.19 % 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: -0.30 (0.15), residues: 3152 helix: 0.66 (0.15), residues: 1216 sheet: -0.88 (0.23), residues: 481 loop : -0.59 (0.17), residues: 1455 ********************** 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 391 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 310 time to evaluate : 2.876 Fit side-chains revert: symmetry clash outliers start: 81 outliers final: 63 residues processed: 372 average time/residue: 1.4242 time to fit residues: 608.9009 Evaluate side-chains 369 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 306 time to evaluate : 2.759 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 49 residues processed: 17 average time/residue: 0.7451 time to fit residues: 19.8026 ------------------------------------------------------------------------------- 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: 0.0970 chunk 76 optimal weight: 1.9990 chunk 231 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 251 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 257 optimal weight: 0.8980 chunk 31 optimal weight: 0.0970 chunk 46 optimal weight: 0.8980 chunk 220 optimal weight: 2.9990 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 HIS ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 431 ASN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 HIS ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 ASN ** 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 = 0.3972 r_free = 0.3972 target = 0.169363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.145323 restraints weight = 48571.712| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.34 r_work: 0.3542 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.6061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 24744 Z= 0.246 Angle : 0.615 10.008 33631 Z= 0.308 Chirality : 0.045 0.206 4007 Planarity : 0.005 0.070 4297 Dihedral : 6.469 171.879 3451 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 2.72 % 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: -0.19 (0.15), residues: 3152 helix: 0.79 (0.15), residues: 1214 sheet: -0.87 (0.23), residues: 487 loop : -0.54 (0.17), residues: 1451 =============================================================================== Job complete usr+sys time: 11409.16 seconds wall clock time: 202 minutes 41.04 seconds (12161.04 seconds total)