Starting phenix.real_space_refine on Tue Mar 19 13:59:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caj_7442/03_2024/6caj_7442_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caj_7442/03_2024/6caj_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_7442/03_2024/6caj_7442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caj_7442/03_2024/6caj_7442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caj_7442/03_2024/6caj_7442_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6caj_7442/03_2024/6caj_7442_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 12.06, per 1000 atoms: 0.50 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: 9.09 Conformation dependent library (CDL) restraints added in 3.8 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: 4.71 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: 8.51 Time building geometry restraints manager: 9.90 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: 14853 34.00 - 68.00: 62 68.00 - 102.00: 14 102.00 - 136.00: 12 136.00 - 170.00: 2 Dihedral angle restraints: 14943 sinusoidal: 5582 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 14940 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: 5.100 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: 0.010 Extract box with map and model: 19.850 Check model and map are aligned: 0.370 Set scattering table: 0.210 Process input model: 63.150 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.180 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:14.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.540 ------------------------------------------------------------------------------- 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 : 10.477 170.000 8853 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 % Allowed : 1.81 % Favored : 97.95 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 272 HIS 0.006 0.001 HIS F 274 PHE 0.019 0.002 PHE C 272 TYR 0.018 0.002 TYR A 78 ARG 0.005 0.001 ARG F 517 *********************** 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 : 2.999 Fit side-chains revert: symmetry clash REVERT: B 53 ASP cc_start: 0.4412 (t0) cc_final: 0.4162 (p0) REVERT: B 104 GLU cc_start: 0.5600 (tt0) cc_final: 0.5291 (tm-30) REVERT: B 269 ARG cc_start: 0.1374 (ttp80) cc_final: 0.1152 (ttp-170) REVERT: B 339 ARG cc_start: 0.1236 (mtp85) cc_final: 0.1032 (ttm-80) REVERT: B 352 HIS cc_start: 0.5278 (m-70) cc_final: 0.5007 (t70) REVERT: J 99 THR cc_start: 0.0757 (t) cc_final: -0.0026 (t) REVERT: H 270 HIS cc_start: 0.3595 (m-70) cc_final: 0.3321 (m170) REVERT: H 292 THR cc_start: 0.1763 (t) cc_final: 0.1558 (p) REVERT: C 149 GLU cc_start: 0.5583 (mt-10) cc_final: 0.5264 (tm-30) REVERT: C 203 MET cc_start: 0.3078 (ttt) cc_final: 0.2629 (tpp) REVERT: C 206 ASN cc_start: 0.4851 (m-40) cc_final: 0.4529 (m110) REVERT: C 251 THR cc_start: 0.3240 (t) cc_final: 0.2800 (t) REVERT: C 309 HIS cc_start: 0.0332 (m90) cc_final: -0.0504 (m-70) REVERT: C 342 GLU cc_start: 0.5093 (mt-10) cc_final: 0.4836 (mt-10) REVERT: F 248 LEU cc_start: 0.3485 (tt) cc_final: 0.3276 (tp) REVERT: F 277 ILE cc_start: 0.4718 (mt) cc_final: 0.4367 (mt) REVERT: F 362 ASP cc_start: 0.4420 (t0) cc_final: 0.4099 (t0) REVERT: F 461 ASP cc_start: 0.2855 (m-30) cc_final: 0.2653 (m-30) REVERT: A 53 ASP cc_start: 0.4342 (t0) cc_final: 0.4010 (p0) REVERT: A 104 GLU cc_start: 0.5504 (tt0) cc_final: 0.5241 (tm-30) REVERT: A 264 PHE cc_start: 0.3768 (t80) cc_final: 0.3566 (t80) REVERT: A 269 ARG cc_start: 0.1298 (ttp80) cc_final: 0.1071 (ttp-170) REVERT: A 352 HIS cc_start: 0.5286 (m-70) cc_final: 0.5014 (t70) REVERT: I 1 MET cc_start: 0.4147 (mmm) cc_final: 0.3931 (ttp) REVERT: I 99 THR cc_start: 0.0479 (t) cc_final: -0.0843 (t) REVERT: G 270 HIS cc_start: 0.3603 (m-70) cc_final: 0.3339 (m170) REVERT: G 292 THR cc_start: 0.1850 (t) cc_final: 0.1641 (p) REVERT: D 149 GLU cc_start: 0.5607 (mt-10) cc_final: 0.5295 (tm-30) REVERT: D 203 MET cc_start: 0.2943 (ttt) cc_final: 0.2502 (tpp) REVERT: D 206 ASN cc_start: 0.4809 (m-40) cc_final: 0.4467 (m110) REVERT: D 251 THR cc_start: 0.3224 (t) cc_final: 0.2786 (t) REVERT: D 309 HIS cc_start: 0.0388 (m90) cc_final: -0.0487 (m-70) REVERT: D 342 GLU cc_start: 0.5034 (mt-10) cc_final: 0.4816 (mt-10) REVERT: E 273 MET cc_start: 0.3322 (mtp) cc_final: 0.3028 (mtp) REVERT: E 324 TYR cc_start: 0.1569 (t80) cc_final: 0.1358 (t80) REVERT: E 362 ASP cc_start: 0.4382 (t0) cc_final: 0.4085 (t0) outliers start: 6 outliers final: 2 residues processed: 832 average time/residue: 1.2971 time to fit residues: 1238.7684 Evaluate side-chains 449 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 447 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain A residue 57 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 0.7980 chunk 239 optimal weight: 0.0670 chunk 132 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 247 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 286 optimal weight: 3.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- 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 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 409 HIS A 410 GLN I 203 HIS I 218 ASN G 213 ASN G 243 GLN G 244 GLN D 150 ASN D 160 HIS D 252 HIS D 286 HIS E 275 ASN E 347 GLN E 406 HIS ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1504 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 24744 Z= 0.245 Angle : 0.626 12.327 33631 Z= 0.313 Chirality : 0.046 0.239 4007 Planarity : 0.005 0.058 4297 Dihedral : 6.452 155.413 3483 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.69 % Allowed : 14.07 % Favored : 81.25 % 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: -1.89 (0.14), residues: 3152 helix: -0.63 (0.14), residues: 1206 sheet: -1.72 (0.23), residues: 455 loop : -1.54 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 476 HIS 0.013 0.002 HIS A 288 PHE 0.026 0.002 PHE I 266 TYR 0.014 0.002 TYR J 210 ARG 0.010 0.001 ARG H 108 *********************** 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 600 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 481 time to evaluate : 2.569 Fit side-chains REVERT: B 104 GLU cc_start: 0.5654 (tt0) cc_final: 0.5419 (tm-30) REVERT: B 269 ARG cc_start: 0.0976 (ttp80) cc_final: 0.0661 (ttp-170) REVERT: H 270 HIS cc_start: 0.3182 (m-70) cc_final: 0.2917 (m170) REVERT: H 292 THR cc_start: 0.1770 (t) cc_final: 0.1404 (p) REVERT: F 254 ASN cc_start: 0.5912 (m110) cc_final: 0.5702 (m-40) REVERT: A 104 GLU cc_start: 0.5662 (tt0) cc_final: 0.5448 (tm-30) REVERT: A 269 ARG cc_start: 0.0955 (ttp80) cc_final: 0.0633 (ttp-170) REVERT: I 99 THR cc_start: 0.0415 (t) cc_final: 0.0078 (t) REVERT: G 270 HIS cc_start: 0.3123 (m-70) cc_final: 0.2814 (m170) REVERT: G 292 THR cc_start: 0.1795 (t) cc_final: 0.1433 (p) outliers start: 119 outliers final: 34 residues processed: 562 average time/residue: 1.2580 time to fit residues: 816.1465 Evaluate side-chains 386 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 352 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 372 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 159 optimal weight: 0.3980 chunk 89 optimal weight: 0.9980 chunk 238 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 287 optimal weight: 0.9990 chunk 310 optimal weight: 0.7980 chunk 256 optimal weight: 1.9990 chunk 285 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 244 GLN C 44 GLN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN F 309 GLN A 216 GLN ** 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 244 GLN D 44 GLN D 206 ASN E 254 ASN E 309 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1455 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24744 Z= 0.233 Angle : 0.610 10.776 33631 Z= 0.303 Chirality : 0.046 0.349 4007 Planarity : 0.005 0.054 4297 Dihedral : 6.597 168.210 3483 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.56 % Allowed : 16.00 % Favored : 78.45 % 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: -1.22 (0.14), residues: 3152 helix: -0.02 (0.15), residues: 1228 sheet: -1.43 (0.22), residues: 503 loop : -1.18 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 37 HIS 0.008 0.001 HIS B 288 PHE 0.017 0.002 PHE D 177 TYR 0.018 0.002 TYR A 296 ARG 0.008 0.001 ARG B 269 *********************** 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 507 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 366 time to evaluate : 2.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 104 GLU cc_start: 0.5610 (tt0) cc_final: 0.5389 (tm-30) REVERT: B 270 ASP cc_start: 0.3998 (m-30) cc_final: 0.3780 (t70) REVERT: A 104 GLU cc_start: 0.5630 (tt0) cc_final: 0.5429 (tm-30) REVERT: I 116 GLU cc_start: 0.4514 (OUTLIER) cc_final: 0.4260 (tp30) outliers start: 141 outliers final: 62 residues processed: 458 average time/residue: 1.3673 time to fit residues: 720.3978 Evaluate side-chains 361 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 298 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 226 SER Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 295 GLU Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 116 GLU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 388 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 284 optimal weight: 2.9990 chunk 216 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 193 optimal weight: 3.9990 chunk 288 optimal weight: 0.9980 chunk 305 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 273 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN F 448 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** D 158 HIS E 254 ASN E 448 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1437 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24744 Z= 0.234 Angle : 0.583 10.341 33631 Z= 0.291 Chirality : 0.045 0.209 4007 Planarity : 0.004 0.055 4297 Dihedral : 6.442 163.207 3483 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 5.48 % Allowed : 17.38 % Favored : 77.15 % 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: -0.77 (0.15), residues: 3152 helix: 0.35 (0.15), residues: 1234 sheet: -1.24 (0.22), residues: 501 loop : -0.90 (0.17), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 37 HIS 0.007 0.001 HIS B 352 PHE 0.020 0.002 PHE C 177 TYR 0.020 0.002 TYR A 128 ARG 0.013 0.001 ARG B 274 *********************** 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 450 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 311 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 104 GLU cc_start: 0.5535 (tt0) cc_final: 0.5320 (tm-30) REVERT: I 116 GLU cc_start: 0.4453 (OUTLIER) cc_final: 0.4222 (tp30) REVERT: G 180 ASP cc_start: 0.3556 (t0) cc_final: 0.3088 (t0) outliers start: 139 outliers final: 57 residues processed: 408 average time/residue: 1.3821 time to fit residues: 644.7532 Evaluate side-chains 343 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 285 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 270 HIS Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 355 ARG Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 116 GLU Chi-restraints excluded: chain I residue 125 ASP Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 270 HIS Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 355 ARG Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 502 THR 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: 0.9980 chunk 4 optimal weight: 0.9980 chunk 227 optimal weight: 7.9990 chunk 126 optimal weight: 0.1980 chunk 260 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 274 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** E 371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1420 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24744 Z= 0.229 Angle : 0.587 10.251 33631 Z= 0.291 Chirality : 0.044 0.224 4007 Planarity : 0.004 0.051 4297 Dihedral : 6.468 164.981 3483 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 5.08 % Allowed : 18.01 % Favored : 76.91 % 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: -0.43 (0.15), residues: 3152 helix: 0.67 (0.15), residues: 1228 sheet: -1.10 (0.22), residues: 501 loop : -0.72 (0.17), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 366 HIS 0.007 0.001 HIS A 352 PHE 0.023 0.002 PHE D 177 TYR 0.020 0.002 TYR B 128 ARG 0.011 0.001 ARG B 274 *********************** 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 443 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 314 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 104 GLU cc_start: 0.5528 (tt0) cc_final: 0.5307 (tm-30) REVERT: J 116 GLU cc_start: 0.4597 (OUTLIER) cc_final: 0.4326 (tp30) REVERT: F 247 GLU cc_start: 0.5292 (OUTLIER) cc_final: 0.4871 (mp0) outliers start: 129 outliers final: 62 residues processed: 407 average time/residue: 1.4269 time to fit residues: 662.6507 Evaluate side-chains 355 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 291 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 270 HIS Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain F residue 247 GLU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 355 ARG Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 270 HIS Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 355 ARG Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 502 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 102 optimal weight: 0.9990 chunk 275 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 190 HIS H 223 ASN C 158 HIS ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 HIS F 422 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 371 ASN ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 HIS G 223 ASN D 138 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1391 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 24744 Z= 0.392 Angle : 0.684 10.482 33631 Z= 0.343 Chirality : 0.048 0.251 4007 Planarity : 0.006 0.072 4297 Dihedral : 7.006 171.158 3483 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.65 % Allowed : 19.19 % Favored : 76.16 % 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: -0.61 (0.15), residues: 3152 helix: 0.42 (0.15), residues: 1228 sheet: -1.05 (0.22), residues: 501 loop : -0.78 (0.17), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP J 37 HIS 0.008 0.001 HIS B 352 PHE 0.032 0.002 PHE D 177 TYR 0.027 0.002 TYR A 128 ARG 0.012 0.001 ARG A 274 *********************** 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 433 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 315 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.6502 (mtt180) cc_final: 0.6157 (ttm110) REVERT: B 104 GLU cc_start: 0.5520 (tt0) cc_final: 0.5290 (tm-30) REVERT: H 103 ARG cc_start: 0.4614 (mmm-85) cc_final: 0.4261 (tpt170) REVERT: C 43 ARG cc_start: 0.4239 (OUTLIER) cc_final: 0.3891 (mtm-85) REVERT: A 54 ARG cc_start: 0.6615 (mtt180) cc_final: 0.6256 (ttm110) REVERT: G 103 ARG cc_start: 0.5085 (mmm-85) cc_final: 0.4505 (tpt170) REVERT: G 108 ARG cc_start: 0.3297 (mtt-85) cc_final: 0.3049 (ptm160) outliers start: 118 outliers final: 76 residues processed: 399 average time/residue: 1.4093 time to fit residues: 640.9758 Evaluate side-chains 375 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 298 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 226 SER Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 355 ARG Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 116 GLU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 203 HIS Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 136 ARG Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 355 ARG Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 502 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 294 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 223 optimal weight: 0.0770 chunk 172 optimal weight: 1.9990 chunk 257 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 chunk 304 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 140 optimal weight: 0.1980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 223 ASN C 150 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 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 150 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1402 moved from start: 0.5756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24744 Z= 0.193 Angle : 0.567 9.966 33631 Z= 0.285 Chirality : 0.044 0.185 4007 Planarity : 0.004 0.071 4297 Dihedral : 6.457 164.376 3483 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.66 % Allowed : 21.39 % Favored : 74.94 % 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: -0.22 (0.15), residues: 3152 helix: 0.81 (0.15), residues: 1218 sheet: -0.96 (0.22), residues: 501 loop : -0.58 (0.17), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 366 HIS 0.007 0.001 HIS B 352 PHE 0.022 0.002 PHE C 177 TYR 0.020 0.001 TYR I 210 ARG 0.014 0.000 ARG H 108 *********************** 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 398 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 305 time to evaluate : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.6488 (mtt180) cc_final: 0.6125 (ttm110) REVERT: B 104 GLU cc_start: 0.5436 (tt0) cc_final: 0.5215 (tm-30) REVERT: C 43 ARG cc_start: 0.4297 (OUTLIER) cc_final: 0.3946 (mtm-85) REVERT: A 54 ARG cc_start: 0.6615 (mtt180) cc_final: 0.6223 (ttm110) REVERT: D 212 ILE cc_start: -0.0457 (OUTLIER) cc_final: -0.0694 (mt) outliers start: 93 outliers final: 56 residues processed: 372 average time/residue: 1.4211 time to fit residues: 602.9845 Evaluate side-chains 339 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 281 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 355 ARG Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 116 GLU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 203 HIS Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 355 ARG Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 502 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 188 optimal weight: 3.9990 chunk 121 optimal weight: 0.0000 chunk 181 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 207 optimal weight: 0.1980 chunk 150 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 239 optimal weight: 3.9990 chunk 277 optimal weight: 0.0770 overall best weight: 0.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** C 44 GLN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 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 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1407 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 24744 Z= 0.168 Angle : 0.550 9.903 33631 Z= 0.274 Chirality : 0.043 0.189 4007 Planarity : 0.004 0.058 4297 Dihedral : 6.226 160.922 3483 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.31 % Allowed : 21.99 % Favored : 74.70 % 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: -0.01 (0.16), residues: 3152 helix: 1.01 (0.15), residues: 1216 sheet: -0.86 (0.23), residues: 487 loop : -0.49 (0.17), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 272 HIS 0.008 0.001 HIS B 352 PHE 0.019 0.001 PHE C 177 TYR 0.017 0.001 TYR A 128 ARG 0.012 0.000 ARG B 274 *********************** 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 391 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 307 time to evaluate : 2.796 Fit side-chains revert: symmetry clash REVERT: B 54 ARG cc_start: 0.6534 (mtt180) cc_final: 0.6117 (ttm110) REVERT: B 104 GLU cc_start: 0.5444 (tt0) cc_final: 0.5236 (tt0) REVERT: C 43 ARG cc_start: 0.4315 (OUTLIER) cc_final: 0.3972 (mtm-85) REVERT: A 54 ARG cc_start: 0.6607 (mtt180) cc_final: 0.6239 (ttm110) outliers start: 84 outliers final: 50 residues processed: 370 average time/residue: 1.3705 time to fit residues: 581.5461 Evaluate side-chains 345 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 294 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 355 ARG Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 203 HIS Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 388 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 291 optimal weight: 0.8980 chunk 266 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 222 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 256 optimal weight: 0.3980 chunk 268 optimal weight: 1.9990 chunk 282 optimal weight: 0.0470 chunk 186 optimal weight: 3.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 13 GLN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1403 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24744 Z= 0.206 Angle : 0.578 10.043 33631 Z= 0.287 Chirality : 0.044 0.214 4007 Planarity : 0.005 0.078 4297 Dihedral : 6.326 162.223 3483 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.11 % Allowed : 22.14 % Favored : 74.74 % 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: 0.02 (0.16), residues: 3152 helix: 0.99 (0.15), residues: 1218 sheet: -0.81 (0.24), residues: 487 loop : -0.44 (0.17), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 366 HIS 0.008 0.001 HIS A 352 PHE 0.023 0.002 PHE D 177 TYR 0.022 0.001 TYR J 210 ARG 0.013 0.000 ARG B 274 *********************** 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 379 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 300 time to evaluate : 2.731 Fit side-chains revert: symmetry clash REVERT: B 54 ARG cc_start: 0.6556 (mtt180) cc_final: 0.6140 (ttm110) REVERT: B 104 GLU cc_start: 0.5447 (tt0) cc_final: 0.5217 (tm-30) REVERT: C 43 ARG cc_start: 0.4314 (OUTLIER) cc_final: 0.3958 (mtm-85) REVERT: A 54 ARG cc_start: 0.6600 (mtt180) cc_final: 0.6229 (ttm110) outliers start: 79 outliers final: 60 residues processed: 358 average time/residue: 1.4003 time to fit residues: 572.0277 Evaluate side-chains 343 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 282 time to evaluate : 2.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 226 SER Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 355 ARG Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 203 HIS Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 388 ILE 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: 2.9990 chunk 142 optimal weight: 1.9990 chunk 208 optimal weight: 0.5980 chunk 314 optimal weight: 0.9980 chunk 289 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 153 optimal weight: 0.2980 chunk 199 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 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 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1388 moved from start: 0.6021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24744 Z= 0.314 Angle : 0.649 9.965 33631 Z= 0.323 Chirality : 0.046 0.223 4007 Planarity : 0.005 0.070 4297 Dihedral : 6.769 166.913 3483 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.39 % Allowed : 21.95 % Favored : 74.67 % 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: -0.16 (0.15), residues: 3152 helix: 0.79 (0.15), residues: 1216 sheet: -0.84 (0.23), residues: 499 loop : -0.49 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 37 HIS 0.008 0.001 HIS A 352 PHE 0.030 0.002 PHE D 177 TYR 0.024 0.002 TYR A 128 ARG 0.012 0.001 ARG B 274 ********************** 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 388 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 302 time to evaluate : 3.858 Fit side-chains revert: symmetry clash REVERT: B 104 GLU cc_start: 0.5458 (tt0) cc_final: 0.5230 (tm-30) REVERT: H 20 MET cc_start: 0.1470 (ttt) cc_final: 0.1210 (tpt) REVERT: H 103 ARG cc_start: 0.4505 (mmm-85) cc_final: 0.4150 (tpt170) REVERT: C 43 ARG cc_start: 0.4252 (OUTLIER) cc_final: 0.3900 (mtm-85) REVERT: I 217 GLU cc_start: 0.3795 (mm-30) cc_final: 0.3383 (mt-10) REVERT: G 20 MET cc_start: 0.1171 (ttt) cc_final: 0.0876 (tpt) REVERT: G 103 ARG cc_start: 0.4912 (mmm-85) cc_final: 0.4307 (tpt170) outliers start: 86 outliers final: 64 residues processed: 367 average time/residue: 1.5224 time to fit residues: 636.4553 Evaluate side-chains 368 residues out of total 2800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 303 time to evaluate : 3.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 226 SER Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 355 ARG Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 203 HIS Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 502 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 267 optimal weight: 0.0770 chunk 76 optimal weight: 0.9980 chunk 231 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 251 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 257 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 220 optimal weight: 0.9980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 HIS B 359 ASN B 376 ASN ** 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** ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.170118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.145061 restraints weight = 35523.336| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.61 r_work: 0.3588 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3468 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.6027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24744 Z= 0.230 Angle : 0.607 9.735 33631 Z= 0.301 Chirality : 0.044 0.219 4007 Planarity : 0.005 0.077 4297 Dihedral : 6.588 163.529 3483 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.19 % Allowed : 22.34 % Favored : 74.47 % 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: -0.07 (0.16), residues: 3152 helix: 0.86 (0.15), residues: 1214 sheet: -0.79 (0.23), residues: 485 loop : -0.46 (0.17), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 366 HIS 0.008 0.001 HIS A 352 PHE 0.026 0.002 PHE C 177 TYR 0.021 0.001 TYR A 128 ARG 0.013 0.001 ARG B 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11526.87 seconds wall clock time: 203 minutes 18.28 seconds (12198.28 seconds total)