Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 13 12:06:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d44_30569/07_2023/7d44_30569_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d44_30569/07_2023/7d44_30569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d44_30569/07_2023/7d44_30569.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d44_30569/07_2023/7d44_30569.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d44_30569/07_2023/7d44_30569_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d44_30569/07_2023/7d44_30569_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 P 2 5.49 5 S 142 5.16 5 C 17918 2.51 5 N 4998 2.21 5 O 5331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 347": "OD1" <-> "OD2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 193": "OE1" <-> "OE2" Residue "D PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 301": "OD1" <-> "OD2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 133": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E ASP 161": "OD1" <-> "OD2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E ASP 177": "OD1" <-> "OD2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E ARG 194": "NH1" <-> "NH2" Residue "E PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 286": "NH1" <-> "NH2" Residue "F TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 49": "OE1" <-> "OE2" Residue "F TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 100": "OD1" <-> "OD2" Residue "F TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 178": "OE1" <-> "OE2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 288": "OD1" <-> "OD2" Residue "G ASP 172": "OD1" <-> "OD2" Residue "G TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 305": "OD1" <-> "OD2" Residue "G TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 344": "NH1" <-> "NH2" Residue "G PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 417": "NH1" <-> "NH2" Residue "G PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 446": "NH1" <-> "NH2" Residue "G ASP 450": "OD1" <-> "OD2" Residue "G PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 517": "NH1" <-> "NH2" Residue "H PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 305": "OD1" <-> "OD2" Residue "H TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 344": "NH1" <-> "NH2" Residue "H TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 417": "NH1" <-> "NH2" Residue "H ARG 446": "NH1" <-> "NH2" Residue "H ASP 458": "OD1" <-> "OD2" Residue "H ASP 459": "OD1" <-> "OD2" Residue "H ASP 490": "OD1" <-> "OD2" Residue "H ARG 517": "NH1" <-> "NH2" Residue "I ASP 53": "OD1" <-> "OD2" Residue "I ARG 65": "NH1" <-> "NH2" Residue "I TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 90": "OE1" <-> "OE2" Residue "I PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 154": "OD1" <-> "OD2" Residue "I ASP 199": "OD1" <-> "OD2" Residue "I ASP 206": "OD1" <-> "OD2" Residue "I PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 236": "OD1" <-> "OD2" Residue "I ASP 246": "OD1" <-> "OD2" Residue "I PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 269": "NH1" <-> "NH2" Residue "I PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 299": "NH1" <-> "NH2" Residue "I ASP 461": "OD1" <-> "OD2" Residue "J ASP 50": "OD1" <-> "OD2" Residue "J ARG 65": "NH1" <-> "NH2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 139": "OD1" <-> "OD2" Residue "J ASP 154": "OD1" <-> "OD2" Residue "J ARG 195": "NH1" <-> "NH2" Residue "J ARG 211": "NH1" <-> "NH2" Residue "J PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 236": "OD1" <-> "OD2" Residue "J PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 269": "NH1" <-> "NH2" Residue "J ARG 299": "NH1" <-> "NH2" Residue "J TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 312": "OD1" <-> "OD2" Residue "J ARG 316": "NH1" <-> "NH2" Residue "J TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 418": "OE1" <-> "OE2" Residue "J ASP 462": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 28391 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2262 Classifications: {'peptide': 293} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2247 Classifications: {'peptide': 291} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2476 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "D" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2538 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2430 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 10, 'TRANS': 332} Chain breaks: 4 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 99 Chain: "F" Number of atoms: 2429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2429 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 10, 'TRANS': 332} Chain breaks: 4 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 100 Chain: "G" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "H" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "I" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3358 Classifications: {'peptide': 427} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 408} Chain: "J" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3373 Classifications: {'peptide': 429} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 409} Chain: "K" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 889 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 4, 'TRANS': 171} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 585 Unresolved non-hydrogen angles: 743 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 18, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 340 Chain: "L" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 889 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 4, 'TRANS': 171} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 585 Unresolved non-hydrogen angles: 743 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 18, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 340 Time building chain proxies: 13.38, per 1000 atoms: 0.47 Number of scatterers: 28391 At special positions: 0 Unit cell: (164.64, 169.05, 191.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 142 16.00 P 2 15.00 O 5331 8.00 N 4998 7.00 C 17918 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: 11.28 Conformation dependent library (CDL) restraints added in 4.3 seconds 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7258 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 37 sheets defined 36.4% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 Processing helix chain 'A' and resid 22 through 35 Processing helix chain 'A' and resid 43 through 57 WARNING: missing atoms! Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 87 through 115 removed outlier: 4.472A pdb=" N ARG A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 160 through 171 removed outlier: 4.232A pdb=" N LEU A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 188 removed outlier: 3.674A pdb=" N VAL A 183 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY A 184 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE A 186 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 188 " --> pdb=" O TYR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 221 Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 248 through 251 No H-bonds generated for 'chain 'A' and resid 248 through 251' Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.931A pdb=" N SER A 297 " --> pdb=" O PRO A 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 16 removed outlier: 5.019A pdb=" N GLU B 8 " --> pdb=" O LYS B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 Processing helix chain 'B' and resid 43 through 46 No H-bonds generated for 'chain 'B' and resid 43 through 46' Processing helix chain 'B' and resid 48 through 59 removed outlier: 4.295A pdb=" N GLY B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 77 removed outlier: 3.962A pdb=" N SER B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 115 removed outlier: 4.105A pdb=" N ARG B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASN B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 removed outlier: 4.002A pdb=" N ALA B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 171 removed outlier: 4.280A pdb=" N LEU B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 189 Processing helix chain 'B' and resid 210 through 222 removed outlier: 4.107A pdb=" N ASN B 213 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLN B 214 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 251 No H-bonds generated for 'chain 'B' and resid 248 through 251' Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 54 through 71 Processing helix chain 'C' and resid 77 through 95 Processing helix chain 'C' and resid 129 through 157 removed outlier: 3.594A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N MET C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLU C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 181 Processing helix chain 'C' and resid 198 through 210 removed outlier: 4.413A pdb=" N LEU C 207 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 228 removed outlier: 4.224A pdb=" N PHE C 223 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N SER C 227 " --> pdb=" O ALA C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 271 through 273 No H-bonds generated for 'chain 'C' and resid 271 through 273' 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 304 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 335 through 343 Processing helix chain 'C' and resid 346 through 350 removed outlier: 4.034A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL C 350 " --> pdb=" O ASP C 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 346 through 350' 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 Processing helix chain 'D' and resid 76 through 95 Processing helix chain 'D' and resid 128 through 145 Processing helix chain 'D' and resid 147 through 158 removed outlier: 4.720A pdb=" N GLN D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLU D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS D 158 " --> pdb=" O GLN D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 181 Processing helix chain 'D' and resid 200 through 210 removed outlier: 4.120A pdb=" N ALA D 210 " --> pdb=" O ASN D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 228 removed outlier: 5.157A pdb=" N SER D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ARG D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 271 through 273 No H-bonds generated for 'chain 'D' and resid 271 through 273' Processing helix chain 'D' and resid 279 through 281 No H-bonds generated for 'chain 'D' and resid 279 through 281' Processing helix chain 'D' and resid 291 through 293 No H-bonds generated for 'chain 'D' and resid 291 through 293' Processing helix chain 'D' and resid 301 through 304 Processing helix chain 'D' and resid 339 through 343 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 35 through 45 Proline residue: E 39 - end of helix removed outlier: 4.330A pdb=" N LEU E 42 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU E 43 " --> pdb=" O PRO E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 66 No H-bonds generated for 'chain 'E' and resid 63 through 66' Processing helix chain 'E' and resid 86 through 96 Proline residue: E 95 - end of helix Processing helix chain 'E' and resid 114 through 123 Processing helix chain 'E' and resid 210 through 216 Processing helix chain 'E' and resid 224 through 227 No H-bonds generated for 'chain 'E' and resid 224 through 227' Processing helix chain 'E' and resid 229 through 237 removed outlier: 4.549A pdb=" N PHE E 237 " --> pdb=" O VAL E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 294 removed outlier: 4.329A pdb=" N TRP E 290 " --> pdb=" O ARG E 286 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU E 293 " --> pdb=" O ARG E 289 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N SER E 294 " --> pdb=" O TRP E 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 45 Processing helix chain 'F' and resid 63 through 67 Processing helix chain 'F' and resid 86 through 93 Processing helix chain 'F' and resid 114 through 122 Processing helix chain 'F' and resid 184 through 189 Processing helix chain 'F' and resid 209 through 217 Processing helix chain 'F' and resid 224 through 235 removed outlier: 5.256A pdb=" N ILE F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) Proline residue: F 230 - end of helix Processing helix chain 'F' and resid 279 through 291 removed outlier: 3.776A pdb=" N ASN F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP F 290 " --> pdb=" O ARG F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 192 through 194 No H-bonds generated for 'chain 'G' and resid 192 through 194' Processing helix chain 'G' and resid 205 through 215 Processing helix chain 'G' and resid 222 through 237 Processing helix chain 'G' and resid 248 through 266 removed outlier: 4.991A pdb=" N VAL G 253 " --> pdb=" O SER G 249 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 271 through 286 Processing helix chain 'G' and resid 293 through 310 Processing helix chain 'G' and resid 313 through 325 removed outlier: 4.286A pdb=" N GLN G 325 " --> pdb=" O ARG G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 351 Processing helix chain 'G' and resid 369 through 379 removed outlier: 3.960A pdb=" N ALA G 379 " --> pdb=" O SER G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 393 removed outlier: 4.674A pdb=" N SER G 392 " --> pdb=" O PRO G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 418 through 430 removed outlier: 4.621A pdb=" N GLN G 422 " --> pdb=" O VAL G 418 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 462 No H-bonds generated for 'chain 'G' and resid 460 through 462' Processing helix chain 'G' and resid 509 through 515 Proline residue: G 513 - end of helix Processing helix chain 'H' and resid 178 through 180 No H-bonds generated for 'chain 'H' and resid 178 through 180' Processing helix chain 'H' and resid 192 through 195 Processing helix chain 'H' and resid 205 through 215 Processing helix chain 'H' and resid 222 through 239 removed outlier: 3.745A pdb=" N ASP H 239 " --> pdb=" O GLN H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 266 removed outlier: 4.573A pdb=" N VAL H 253 " --> pdb=" O SER H 249 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 271 through 286 Processing helix chain 'H' and resid 293 through 310 Processing helix chain 'H' and resid 313 through 326 removed outlier: 4.754A pdb=" N GLN H 325 " --> pdb=" O ARG H 321 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS H 326 " --> pdb=" O PHE H 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 349 Processing helix chain 'H' and resid 370 through 379 removed outlier: 4.152A pdb=" N ALA H 379 " --> pdb=" O SER H 375 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 396 removed outlier: 5.744A pdb=" N SER H 392 " --> pdb=" O PRO H 389 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU H 395 " --> pdb=" O SER H 392 " (cutoff:3.500A) Proline residue: H 396 - end of helix Processing helix chain 'H' and resid 420 through 429 Processing helix chain 'H' and resid 460 through 462 No H-bonds generated for 'chain 'H' and resid 460 through 462' Processing helix chain 'H' and resid 509 through 511 No H-bonds generated for 'chain 'H' and resid 509 through 511' Processing helix chain 'H' and resid 513 through 516 No H-bonds generated for 'chain 'H' and resid 513 through 516' Processing helix chain 'I' and resid 59 through 62 No H-bonds generated for 'chain 'I' and resid 59 through 62' Processing helix chain 'I' and resid 75 through 86 Processing helix chain 'I' and resid 99 through 107 Processing helix chain 'I' and resid 131 through 140 Processing helix chain 'I' and resid 162 through 175 Processing helix chain 'I' and resid 228 through 233 Processing helix chain 'I' and resid 254 through 261 Processing helix chain 'I' and resid 269 through 278 Processing helix chain 'I' and resid 303 through 313 Processing helix chain 'I' and resid 331 through 333 No H-bonds generated for 'chain 'I' and resid 331 through 333' Processing helix chain 'I' and resid 339 through 341 No H-bonds generated for 'chain 'I' and resid 339 through 341' Processing helix chain 'J' and resid 59 through 61 No H-bonds generated for 'chain 'J' and resid 59 through 61' Processing helix chain 'J' and resid 65 through 67 No H-bonds generated for 'chain 'J' and resid 65 through 67' Processing helix chain 'J' and resid 75 through 86 Processing helix chain 'J' and resid 99 through 108 removed outlier: 4.407A pdb=" N LYS J 108 " --> pdb=" O GLU J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 141 Processing helix chain 'J' and resid 162 through 174 Processing helix chain 'J' and resid 197 through 199 No H-bonds generated for 'chain 'J' and resid 197 through 199' Processing helix chain 'J' and resid 228 through 233 Processing helix chain 'J' and resid 254 through 262 removed outlier: 4.260A pdb=" N ASP J 262 " --> pdb=" O GLN J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 278 Processing helix chain 'J' and resid 303 through 315 removed outlier: 3.966A pdb=" N ARG J 315 " --> pdb=" O ALA J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 331 through 333 No H-bonds generated for 'chain 'J' and resid 331 through 333' Processing helix chain 'J' and resid 339 through 341 No H-bonds generated for 'chain 'J' and resid 339 through 341' Processing helix chain 'K' and resid 54 through 56 No H-bonds generated for 'chain 'K' and resid 54 through 56' Processing helix chain 'K' and resid 60 through 64 Processing helix chain 'K' and resid 91 through 117 Processing helix chain 'K' and resid 123 through 140 Processing helix chain 'K' and resid 146 through 156 removed outlier: 4.989A pdb=" N VAL K 156 " --> pdb=" O PHE K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 169 through 178 Processing helix chain 'L' and resid 53 through 56 removed outlier: 3.738A pdb=" N ARG L 56 " --> pdb=" O ARG L 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 53 through 56' Processing helix chain 'L' and resid 91 through 117 removed outlier: 3.933A pdb=" N VAL L 117 " --> pdb=" O HIS L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 140 Processing helix chain 'L' and resid 148 through 154 Processing helix chain 'L' and resid 163 through 165 No H-bonds generated for 'chain 'L' and resid 163 through 165' Processing helix chain 'L' and resid 169 through 178 Processing sheet with id= A, first strand: chain 'A' and resid 123 through 126 Processing sheet with id= B, first strand: chain 'A' and resid 193 through 196 removed outlier: 6.653A pdb=" N LEU A 283 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 206 through 209 Processing sheet with id= D, first strand: chain 'B' and resid 123 through 127 removed outlier: 7.540A pdb=" N VAL B 152 " --> pdb=" O PRO B 174 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR B 176 " --> pdb=" O VAL B 152 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 193 through 196 removed outlier: 3.518A pdb=" N VAL B 229 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU B 283 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 207 through 209 Processing sheet with id= G, first strand: chain 'C' and resid 329 through 332 removed outlier: 3.782A pdb=" N LYS C 231 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE C 168 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N HIS C 188 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N THR C 167 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE C 190 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 246 through 248 Processing sheet with id= I, first strand: chain 'D' and resid 189 through 193 Processing sheet with id= J, first strand: chain 'D' and resid 231 through 234 removed outlier: 7.310A pdb=" N ILE D 234 " --> pdb=" O PRO D 264 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE D 266 " --> pdb=" O ILE D 234 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 246 through 248 Processing sheet with id= L, first strand: chain 'D' and resid 324 through 326 Processing sheet with id= M, first strand: chain 'E' and resid 100 through 103 removed outlier: 7.307A pdb=" N VAL E 76 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N THR E 55 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE E 78 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 129 through 132 removed outlier: 7.644A pdb=" N TYR E 264 " --> pdb=" O MET E 130 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N MET E 132 " --> pdb=" O TYR E 264 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE E 266 " --> pdb=" O MET E 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 193 through 196 removed outlier: 5.760A pdb=" N ASP E 161 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU E 167 " --> pdb=" O ASP E 161 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 52 through 54 removed outlier: 6.324A pdb=" N VAL F 76 " --> pdb=" O VAL F 53 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'F' and resid 101 through 103 Processing sheet with id= R, first strand: chain 'F' and resid 169 through 171 Processing sheet with id= S, first strand: chain 'G' and resid 360 through 362 removed outlier: 3.517A pdb=" N LEU G 386 " --> pdb=" O VAL G 360 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP G 362 " --> pdb=" O LEU G 386 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'G' and resid 414 through 417 Processing sheet with id= U, first strand: chain 'G' and resid 500 through 502 Processing sheet with id= V, first strand: chain 'H' and resid 401 through 404 Processing sheet with id= W, first strand: chain 'H' and resid 414 through 416 Processing sheet with id= X, first strand: chain 'H' and resid 500 through 502 Processing sheet with id= Y, first strand: chain 'I' and resid 149 through 151 removed outlier: 6.153A pdb=" N GLU I 90 " --> pdb=" O ALA I 45 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU I 47 " --> pdb=" O GLU I 90 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE I 92 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL I 119 " --> pdb=" O THR I 91 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL I 93 " --> pdb=" O VAL I 119 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG I 121 " --> pdb=" O VAL I 93 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 155 through 157 Processing sheet with id= AA, first strand: chain 'I' and resid 288 through 292 Processing sheet with id= AB, first strand: chain 'I' and resid 239 through 241 Processing sheet with id= AC, first strand: chain 'I' and resid 373 through 375 Processing sheet with id= AD, first strand: chain 'J' and resid 44 through 48 removed outlier: 6.309A pdb=" N GLU J 90 " --> pdb=" O ALA J 45 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU J 47 " --> pdb=" O GLU J 90 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N PHE J 92 " --> pdb=" O LEU J 47 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'J' and resid 185 through 187 Processing sheet with id= AF, first strand: chain 'J' and resid 239 through 241 removed outlier: 5.631A pdb=" N ASP J 206 " --> pdb=" O VAL J 212 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL J 212 " --> pdb=" O ASP J 206 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 390 through 392 Processing sheet with id= AH, first strand: chain 'K' and resid 67 through 71 removed outlier: 6.944A pdb=" N TYR K 32 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE K 82 " --> pdb=" O MET K 44 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP K 83 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG K 74 " --> pdb=" O ASP K 83 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N SER K 85 " --> pdb=" O VAL K 72 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N VAL K 72 " --> pdb=" O SER K 85 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 19 through 23 removed outlier: 3.670A pdb=" N ARG L 66 " --> pdb=" O VAL L 23 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 30 through 34 Processing sheet with id= AK, first strand: chain 'L' and resid 74 through 76 978 hydrogen bonds defined for protein. 2736 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: 8.25 Time building geometry restraints manager: 12.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9599 1.34 - 1.46: 5112 1.46 - 1.58: 13932 1.58 - 1.70: 8 1.70 - 1.81: 216 Bond restraints: 28867 Sorted by residual: bond pdb=" C SER J 188 " pdb=" N SER J 189 " ideal model delta sigma weight residual 1.329 1.252 0.077 1.86e-02 2.89e+03 1.71e+01 bond pdb=" CA LEU D 303 " pdb=" C LEU D 303 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.34e-02 5.57e+03 9.89e+00 bond pdb=" CA GLU D 157 " pdb=" C GLU D 157 " ideal model delta sigma weight residual 1.524 1.483 0.040 1.29e-02 6.01e+03 9.65e+00 bond pdb=" CA SER H 481 " pdb=" C SER H 481 " ideal model delta sigma weight residual 1.523 1.488 0.035 1.34e-02 5.57e+03 6.98e+00 bond pdb=" CA HIS D 260 " pdb=" C HIS D 260 " ideal model delta sigma weight residual 1.522 1.489 0.033 1.40e-02 5.10e+03 5.71e+00 ... (remaining 28862 not shown) Histogram of bond angle deviations from ideal: 98.71 - 105.78: 574 105.78 - 112.85: 16034 112.85 - 119.92: 9384 119.92 - 126.99: 12965 126.99 - 134.06: 268 Bond angle restraints: 39225 Sorted by residual: angle pdb=" C PHE K 12 " pdb=" N PRO K 13 " pdb=" CA PRO K 13 " ideal model delta sigma weight residual 119.84 131.02 -11.18 1.25e+00 6.40e-01 8.00e+01 angle pdb=" N GLU K 14 " pdb=" CA GLU K 14 " pdb=" C GLU K 14 " ideal model delta sigma weight residual 108.74 116.72 -7.98 1.38e+00 5.25e-01 3.35e+01 angle pdb=" C GLU K 14 " pdb=" N VAL K 15 " pdb=" CA VAL K 15 " ideal model delta sigma weight residual 120.35 128.24 -7.89 1.39e+00 5.18e-01 3.22e+01 angle pdb=" C LEU C 178 " pdb=" N LYS C 179 " pdb=" CA LYS C 179 " ideal model delta sigma weight residual 121.94 111.23 10.71 2.00e+00 2.50e-01 2.87e+01 angle pdb=" N VAL C 225 " pdb=" CA VAL C 225 " pdb=" C VAL C 225 " ideal model delta sigma weight residual 113.20 108.63 4.57 9.60e-01 1.09e+00 2.26e+01 ... (remaining 39220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 15567 17.51 - 35.03: 1610 35.03 - 52.54: 288 52.54 - 70.06: 34 70.06 - 87.57: 22 Dihedral angle restraints: 17521 sinusoidal: 6374 harmonic: 11147 Sorted by residual: dihedral pdb=" CA GLU K 14 " pdb=" C GLU K 14 " pdb=" N VAL K 15 " pdb=" CA VAL K 15 " ideal model delta harmonic sigma weight residual -180.00 -137.21 -42.79 0 5.00e+00 4.00e-02 7.32e+01 dihedral pdb=" CA HIS D 125 " pdb=" C HIS D 125 " pdb=" N TYR D 126 " pdb=" CA TYR D 126 " ideal model delta harmonic sigma weight residual -180.00 -153.91 -26.09 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA SER C 284 " pdb=" C SER C 284 " pdb=" N PHE C 285 " pdb=" CA PHE C 285 " ideal model delta harmonic sigma weight residual 180.00 -154.08 -25.92 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 17518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2669 0.036 - 0.073: 1333 0.073 - 0.109: 493 0.109 - 0.145: 151 0.145 - 0.182: 11 Chirality restraints: 4657 Sorted by residual: chirality pdb=" CA PRO A 293 " pdb=" N PRO A 293 " pdb=" C PRO A 293 " pdb=" CB PRO A 293 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CA VAL I 238 " pdb=" N VAL I 238 " pdb=" C VAL I 238 " pdb=" CB VAL I 238 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA ILE A 207 " pdb=" N ILE A 207 " pdb=" C ILE A 207 " pdb=" CB ILE A 207 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 4654 not shown) Planarity restraints: 5083 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 345 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO D 346 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 346 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 346 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 395 " 0.045 5.00e-02 4.00e+02 6.82e-02 7.44e+00 pdb=" N PRO H 396 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO H 396 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO H 396 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 395 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO G 396 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO G 396 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 396 " -0.037 5.00e-02 4.00e+02 ... (remaining 5080 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 546 2.62 - 3.19: 28611 3.19 - 3.76: 43901 3.76 - 4.33: 59257 4.33 - 4.90: 95856 Nonbonded interactions: 228171 Sorted by model distance: nonbonded pdb=" OG SER G 416 " pdb=" OG1 THR G 420 " model vdw 2.049 2.440 nonbonded pdb=" OD2 ASP F 161 " pdb=" OG1 THR F 163 " model vdw 2.089 2.440 nonbonded pdb=" O ASP F 288 " pdb=" N ASP F 292 " model vdw 2.111 2.520 nonbonded pdb=" OG SER J 130 " pdb=" OE1 GLN J 267 " model vdw 2.113 2.440 nonbonded pdb=" ND2 ASN A 203 " pdb=" OH TYR A 275 " model vdw 2.123 2.520 ... (remaining 228166 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' and (resid 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ )) or resid 29 \ through 253 or resid 268 through 305)) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 8 through 343 or (resid 344 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 345 through 351)) selection = (chain 'D' and (resid 8 through 98 or resid 126 through 351)) } ncs_group { reference = (chain 'E' and (resid 1 through 263 or (resid 264 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 265 through 444)) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = (chain 'J' and resid 41 through 467) } ncs_group { reference = chain 'K' selection = chain 'L' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 8.180 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 67.020 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.160 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: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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 : 0.006 0.091 28867 Z= 0.397 Angle : 0.857 11.180 39225 Z= 0.504 Chirality : 0.049 0.182 4657 Planarity : 0.005 0.072 5083 Dihedral : 14.780 87.573 10263 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 16.34 % Favored : 83.61 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.25 (0.11), residues: 3771 helix: -2.48 (0.11), residues: 1365 sheet: -4.09 (0.20), residues: 409 loop : -4.24 (0.11), residues: 1997 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 366 time to evaluate : 3.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 373 average time/residue: 0.4130 time to fit residues: 243.7081 Evaluate side-chains 247 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 242 time to evaluate : 3.348 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2475 time to fit residues: 6.8281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 0.3980 chunk 285 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 0.2980 chunk 192 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 295 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 179 optimal weight: 20.0000 chunk 219 optimal weight: 3.9990 chunk 342 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 208 ASN B 213 ASN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 HIS D 97 HIS D 119 ASN D 125 HIS D 158 HIS ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 HIS E 274 ASN F 60 GLN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN F 283 ASN G 166 GLN G 189 GLN G 213 GLN G 254 ASN G 265 GLN G 281 ASN G 325 GLN G 430 HIS ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 479 HIS H 194 GLN H 234 GLN H 265 GLN ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 GLN H 430 HIS ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 255 GLN ** I 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 388 ASN J 44 GLN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 158 ASN J 279 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 28867 Z= 0.256 Angle : 0.662 9.348 39225 Z= 0.341 Chirality : 0.046 0.180 4657 Planarity : 0.005 0.071 5083 Dihedral : 5.922 49.173 4090 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.50 % Favored : 89.47 % Rotamer Outliers : 2.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.12), residues: 3771 helix: -1.13 (0.13), residues: 1369 sheet: -3.77 (0.21), residues: 409 loop : -3.60 (0.12), residues: 1993 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 279 time to evaluate : 3.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 34 residues processed: 320 average time/residue: 0.3643 time to fit residues: 195.2868 Evaluate side-chains 277 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 243 time to evaluate : 3.553 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 1 residues processed: 34 average time/residue: 0.2579 time to fit residues: 20.7364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 284 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 94 optimal weight: 0.0980 chunk 342 optimal weight: 0.5980 chunk 370 optimal weight: 5.9990 chunk 305 optimal weight: 1.9990 chunk 340 optimal weight: 0.0870 chunk 116 optimal weight: 0.7980 chunk 275 optimal weight: 7.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN D 125 HIS ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 GLN F 236 GLN F 274 ASN G 189 GLN ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 285 ASN ** I 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 28867 Z= 0.199 Angle : 0.617 8.764 39225 Z= 0.316 Chirality : 0.045 0.159 4657 Planarity : 0.004 0.063 5083 Dihedral : 5.502 48.392 4090 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.47 % Favored : 90.51 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.13), residues: 3771 helix: -0.43 (0.14), residues: 1368 sheet: -3.52 (0.21), residues: 427 loop : -3.18 (0.13), residues: 1976 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 304 time to evaluate : 3.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 19 residues processed: 338 average time/residue: 0.3483 time to fit residues: 199.8307 Evaluate side-chains 279 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 260 time to evaluate : 3.059 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 1 residues processed: 19 average time/residue: 0.2609 time to fit residues: 13.1896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 5.9990 chunk 257 optimal weight: 0.6980 chunk 177 optimal weight: 0.0060 chunk 37 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 chunk 344 optimal weight: 20.0000 chunk 364 optimal weight: 1.9990 chunk 179 optimal weight: 20.0000 chunk 326 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN F 274 ASN G 166 GLN ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 GLN ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 341 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 28867 Z= 0.214 Angle : 0.605 7.958 39225 Z= 0.309 Chirality : 0.045 0.165 4657 Planarity : 0.004 0.063 5083 Dihedral : 5.344 47.803 4090 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.33 % Favored : 90.64 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.13), residues: 3771 helix: -0.08 (0.14), residues: 1361 sheet: -3.33 (0.21), residues: 443 loop : -2.99 (0.13), residues: 1967 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 277 time to evaluate : 3.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 33 residues processed: 324 average time/residue: 0.3367 time to fit residues: 187.2012 Evaluate side-chains 284 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 251 time to evaluate : 3.000 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 1 residues processed: 33 average time/residue: 0.2599 time to fit residues: 20.6793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 6.9990 chunk 206 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 271 optimal weight: 0.8980 chunk 150 optimal weight: 50.0000 chunk 310 optimal weight: 0.0980 chunk 251 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 186 optimal weight: 20.0000 chunk 327 optimal weight: 0.0770 chunk 91 optimal weight: 0.9980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN B 13 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 ASN ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 HIS ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 304 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 28867 Z= 0.166 Angle : 0.573 9.207 39225 Z= 0.292 Chirality : 0.044 0.152 4657 Planarity : 0.004 0.062 5083 Dihedral : 5.019 47.247 4090 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.14), residues: 3771 helix: 0.24 (0.14), residues: 1377 sheet: -3.15 (0.21), residues: 469 loop : -2.71 (0.14), residues: 1925 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 296 time to evaluate : 3.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 20 residues processed: 334 average time/residue: 0.3668 time to fit residues: 206.8822 Evaluate side-chains 275 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 255 time to evaluate : 3.279 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 1 residues processed: 20 average time/residue: 0.2682 time to fit residues: 14.4274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 5.9990 chunk 328 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 213 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 364 optimal weight: 0.0170 chunk 302 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 120 optimal weight: 0.0980 chunk 191 optimal weight: 3.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN G 166 GLN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 GLN ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 285 ASN I 384 HIS I 410 GLN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 28867 Z= 0.182 Angle : 0.581 9.008 39225 Z= 0.295 Chirality : 0.044 0.149 4657 Planarity : 0.004 0.063 5083 Dihedral : 4.919 46.389 4090 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.14), residues: 3771 helix: 0.41 (0.14), residues: 1365 sheet: -3.02 (0.22), residues: 432 loop : -2.59 (0.13), residues: 1974 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 269 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 26 residues processed: 301 average time/residue: 0.3467 time to fit residues: 178.7997 Evaluate side-chains 273 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 247 time to evaluate : 3.755 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 1 residues processed: 26 average time/residue: 0.2863 time to fit residues: 18.3310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 0.0370 chunk 41 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 266 optimal weight: 0.0570 chunk 206 optimal weight: 0.9980 chunk 307 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 363 optimal weight: 20.0000 chunk 227 optimal weight: 7.9990 chunk 221 optimal weight: 0.0170 chunk 167 optimal weight: 8.9990 overall best weight: 0.3814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 223 ASN B 13 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 HIS C 277 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 HIS ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN G 411 ASN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 28867 Z= 0.160 Angle : 0.570 10.095 39225 Z= 0.288 Chirality : 0.044 0.145 4657 Planarity : 0.004 0.064 5083 Dihedral : 4.753 45.483 4090 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.14), residues: 3771 helix: 0.62 (0.14), residues: 1361 sheet: -2.80 (0.22), residues: 436 loop : -2.42 (0.14), residues: 1974 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 277 time to evaluate : 3.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 20 residues processed: 303 average time/residue: 0.3564 time to fit residues: 185.0145 Evaluate side-chains 267 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 247 time to evaluate : 3.536 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 1 residues processed: 20 average time/residue: 0.2750 time to fit residues: 14.5544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 217 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 231 optimal weight: 0.0040 chunk 247 optimal weight: 0.3980 chunk 179 optimal weight: 20.0000 chunk 33 optimal weight: 0.0770 chunk 285 optimal weight: 1.9990 overall best weight: 0.3950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS A 223 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN G 166 GLN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 GLN ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 28867 Z= 0.163 Angle : 0.578 10.165 39225 Z= 0.290 Chirality : 0.044 0.170 4657 Planarity : 0.004 0.062 5083 Dihedral : 4.669 44.200 4090 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.14), residues: 3771 helix: 0.70 (0.14), residues: 1360 sheet: -2.60 (0.23), residues: 437 loop : -2.28 (0.14), residues: 1974 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 283 time to evaluate : 3.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 9 residues processed: 305 average time/residue: 0.3693 time to fit residues: 189.4750 Evaluate side-chains 266 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 257 time to evaluate : 3.304 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.2938 time to fit residues: 9.5083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 0.5980 chunk 348 optimal weight: 6.9990 chunk 317 optimal weight: 0.0030 chunk 338 optimal weight: 6.9990 chunk 203 optimal weight: 0.9980 chunk 147 optimal weight: 0.2980 chunk 265 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 305 optimal weight: 2.9990 chunk 320 optimal weight: 0.0470 chunk 337 optimal weight: 6.9990 overall best weight: 0.3688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS A 223 ASN B 13 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 196 HIS F 274 ASN G 166 GLN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 28867 Z= 0.161 Angle : 0.588 12.899 39225 Z= 0.291 Chirality : 0.044 0.178 4657 Planarity : 0.004 0.059 5083 Dihedral : 4.572 43.394 4090 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.14), residues: 3771 helix: 0.85 (0.15), residues: 1349 sheet: -2.48 (0.23), residues: 442 loop : -2.19 (0.14), residues: 1980 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 278 time to evaluate : 3.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 291 average time/residue: 0.3631 time to fit residues: 179.3584 Evaluate side-chains 261 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 249 time to evaluate : 3.329 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.2851 time to fit residues: 10.6755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 0.5980 chunk 358 optimal weight: 0.0570 chunk 218 optimal weight: 0.7980 chunk 169 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 375 optimal weight: 0.9980 chunk 345 optimal weight: 0.3980 chunk 299 optimal weight: 0.0020 chunk 31 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 183 optimal weight: 30.0000 overall best weight: 0.3706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN D 125 HIS ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN G 166 GLN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 GLN H 238 GLN ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 28867 Z= 0.166 Angle : 0.598 13.833 39225 Z= 0.292 Chirality : 0.044 0.192 4657 Planarity : 0.004 0.062 5083 Dihedral : 4.551 42.747 4090 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.14), residues: 3771 helix: 0.82 (0.15), residues: 1362 sheet: -2.35 (0.24), residues: 432 loop : -2.15 (0.14), residues: 1977 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 271 time to evaluate : 3.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 278 average time/residue: 0.3742 time to fit residues: 179.2936 Evaluate side-chains 263 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 254 time to evaluate : 3.289 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.2977 time to fit residues: 9.1926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.2126 > 50: distance: 82 - 87: 6.877 distance: 87 - 88: 13.280 distance: 88 - 89: 14.914 distance: 88 - 91: 10.826 distance: 89 - 90: 4.934 distance: 89 - 95: 20.995 distance: 91 - 92: 8.339 distance: 92 - 93: 10.529 distance: 92 - 94: 9.821 distance: 95 - 96: 8.303 distance: 96 - 97: 16.697 distance: 96 - 99: 14.042 distance: 97 - 98: 25.859 distance: 97 - 103: 37.695 distance: 99 - 100: 25.991 distance: 99 - 101: 8.621 distance: 100 - 102: 31.636 distance: 103 - 104: 5.837 distance: 104 - 105: 14.982 distance: 104 - 107: 3.666 distance: 105 - 106: 12.453 distance: 105 - 110: 10.072 distance: 107 - 108: 6.366 distance: 107 - 109: 17.660 distance: 110 - 111: 16.339 distance: 111 - 112: 17.723 distance: 111 - 114: 12.711 distance: 112 - 113: 17.898 distance: 112 - 118: 12.957 distance: 114 - 115: 25.039 distance: 115 - 116: 28.967 distance: 115 - 117: 24.525 distance: 118 - 119: 28.364 distance: 118 - 124: 34.080 distance: 119 - 120: 25.624 distance: 119 - 122: 18.664 distance: 120 - 121: 12.434 distance: 120 - 125: 33.632 distance: 122 - 123: 25.392 distance: 123 - 124: 16.427 distance: 125 - 126: 5.069 distance: 126 - 127: 14.382 distance: 126 - 129: 16.808 distance: 127 - 128: 8.434 distance: 127 - 134: 10.849 distance: 129 - 130: 12.458 distance: 130 - 131: 10.702 distance: 131 - 132: 8.732 distance: 131 - 133: 17.376 distance: 134 - 135: 22.558 distance: 135 - 136: 23.108 distance: 136 - 137: 9.742 distance: 136 - 138: 3.220 distance: 138 - 139: 15.478 distance: 139 - 140: 18.305 distance: 139 - 142: 7.133 distance: 140 - 141: 14.612 distance: 140 - 144: 17.032 distance: 142 - 143: 9.896 distance: 144 - 145: 9.896 distance: 145 - 146: 8.657 distance: 145 - 148: 6.969 distance: 146 - 147: 17.754 distance: 146 - 151: 21.196 distance: 148 - 149: 22.132 distance: 148 - 150: 18.829 distance: 151 - 152: 17.532 distance: 152 - 153: 10.098 distance: 152 - 155: 7.560 distance: 153 - 154: 22.362 distance: 153 - 159: 7.220 distance: 155 - 156: 21.946 distance: 155 - 157: 29.676 distance: 156 - 158: 19.555