Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 19:49:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o85_0651/04_2023/6o85_0651_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o85_0651/04_2023/6o85_0651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o85_0651/04_2023/6o85_0651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o85_0651/04_2023/6o85_0651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o85_0651/04_2023/6o85_0651_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o85_0651/04_2023/6o85_0651_updated.pdb" } resolution = 3.03 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= 0.067 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 124 5.16 5 Cl 4 4.86 5 C 18349 2.51 5 N 4832 2.21 5 O 5267 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C GLU 33": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C GLU 143": "OE1" <-> "OE2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 157": "OE1" <-> "OE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "E PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 397": "OE1" <-> "OE2" Residue "F GLU 295": "OE1" <-> "OE2" Residue "F GLU 299": "OE1" <-> "OE2" Residue "F PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 445": "OE1" <-> "OE2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "I GLU 49": "OE1" <-> "OE2" Residue "I GLU 116": "OE1" <-> "OE2" Residue "J GLU 49": "OE1" <-> "OE2" Residue "J GLU 116": "OE1" <-> "OE2" Residue "L ARG 56": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 28576 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3172 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 407} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 151 Chain: "B" Number of atoms: 3994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 3994 Classifications: {'peptide': 590} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 177} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 567} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 730 Unresolved non-hydrogen angles: 946 Unresolved non-hydrogen dihedrals: 591 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 9, 'GLU:plan': 24, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 461 Chain: "C" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2415 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 20, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2425 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 20, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "E" Number of atoms: 2712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2712 Classifications: {'peptide': 357} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 338} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 24, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "F" Number of atoms: 2713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2713 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 338} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'ARG:plan': 24, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "G" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2025 Classifications: {'peptide': 285} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 50} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 12, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 97 Chain: "H" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2025 Classifications: {'peptide': 285} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 50} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 12, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 97 Chain: "I" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1609 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 9, 'TRANS': 230} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 185 Chain: "J" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1609 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 9, 'TRANS': 230} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 185 Chain: "L" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 1651 Classifications: {'peptide': 275} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 168} Link IDs: {'PTRANS': 9, 'TRANS': 265} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 577 Unresolved non-hydrogen angles: 740 Unresolved non-hydrogen dihedrals: 445 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 25, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 296 Chain: "S" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 2096 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 329} Link IDs: {'PTRANS': 18, 'TRANS': 391} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1075 Unresolved non-hydrogen angles: 1375 Unresolved non-hydrogen dihedrals: 846 Unresolved non-hydrogen chiralities: 144 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 15, 'TYR:plan': 6, 'ASN:plan1': 14, 'HIS:plan': 9, 'PHE:plan': 6, 'GLU:plan': 26, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 443 Chain: "d" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 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: 15.30, per 1000 atoms: 0.54 Number of scatterers: 28576 At special positions: 0 Unit cell: (123.3, 149.604, 228.516, 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 124 16.00 O 5267 8.00 N 4832 7.00 C 18349 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: 10.67 Conformation dependent library (CDL) restraints added in 4.6 seconds 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7786 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 149 helices and 48 sheets defined 37.4% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... 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 131 through 141 Processing helix chain 'A' and resid 162 through 174 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 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' 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 106 Processing helix chain 'B' and resid 131 through 141 Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 255 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 'B' and resid 550 through 566 Processing helix chain 'B' and resid 571 through 585 Processing helix chain 'B' and resid 589 through 605 Proline residue: B 604 - end of helix Processing helix chain 'B' and resid 614 through 627 Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 629 through 635 Processing helix chain 'B' and resid 639 through 655 Processing helix chain 'B' and resid 657 through 670 removed outlier: 5.153A pdb=" N ILE B 661 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA B 664 " --> pdb=" O ILE B 661 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL B 666 " --> pdb=" O MET B 663 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET B 668 " --> pdb=" O LYS B 665 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE B 670 " --> pdb=" O LEU B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 686 Processing helix chain 'B' and resid 693 through 698 Processing helix chain 'B' and resid 701 through 714 Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 31 through 46 Processing helix chain 'C' and resid 54 through 71 Processing helix chain 'C' and resid 77 through 97 Processing helix chain 'C' and resid 129 through 145 Processing helix chain 'C' and resid 148 through 153 Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 172 through 183 removed outlier: 4.565A pdb=" N ARG C 183 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 222 through 225 No H-bonds generated for 'chain 'C' and resid 222 through 225' Processing helix chain 'C' and resid 251 through 260 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: 3.918A pdb=" N ILE C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N TYR C 337 " --> pdb=" O SER C 334 " (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 'D' and resid 9 through 24 Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 54 through 71 removed outlier: 3.705A pdb=" N ARG D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 97 Processing helix chain 'D' and resid 127 through 144 Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 172 through 183 removed outlier: 4.261A pdb=" N ARG D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 207 Processing helix chain 'D' and resid 219 through 225 removed outlier: 4.024A pdb=" N ILE D 222 " --> pdb=" O ASP D 219 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N PHE D 223 " --> pdb=" O ALA D 220 " (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 336 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 192 through 195 removed outlier: 3.875A 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 Processing helix chain 'E' and resid 248 through 266 removed outlier: 4.529A 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: 5.395A pdb=" N ALA E 315 " --> pdb=" O LYS E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 352 Processing helix chain 'E' and resid 368 through 378 removed outlier: 3.564A pdb=" N THR E 372 " --> pdb=" O GLY E 369 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL E 377 " --> pdb=" O ARG E 374 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N HIS E 378 " --> pdb=" O SER E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 394 No H-bonds generated for 'chain 'E' and resid 391 through 394' 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 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 509 through 517 Proline residue: E 513 - end of helix Processing helix chain 'F' and resid 192 through 195 removed outlier: 3.579A 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 Processing helix chain 'F' and resid 248 through 266 removed outlier: 4.331A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) removed outlier: 3.803A 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 284 Processing helix chain 'F' and resid 293 through 324 removed outlier: 5.398A pdb=" N ALA F 315 " --> pdb=" O LYS F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 352 Processing helix chain 'F' and resid 369 through 377 Processing helix chain 'F' and resid 391 through 394 No H-bonds generated for 'chain 'F' and resid 391 through 394' 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 Proline residue: F 513 - end of helix Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'G' and resid 43 through 59 WARNING: missing atoms! Processing helix chain 'G' and resid 63 through 82 Processing helix chain 'G' and resid 86 through 105 removed outlier: 4.013A pdb=" N LYS G 91 " --> pdb=" O SER G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 118 removed outlier: 4.914A pdb=" N THR G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N PHE G 118 " --> pdb=" O LEU G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 143 Processing helix chain 'G' and resid 161 through 170 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 213 through 221 Processing helix chain 'G' and resid 248 through 250 No H-bonds generated for 'chain 'G' and resid 248 through 250' 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 293 through 303 removed outlier: 3.701A pdb=" N VAL G 296 " --> pdb=" O PRO G 293 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER G 297 " --> pdb=" O SER G 294 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS G 302 " --> pdb=" O GLU G 299 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU G 303 " --> pdb=" O LEU G 300 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 22 through 35 Processing helix chain 'H' and resid 43 through 59 WARNING: missing atoms! Processing helix chain 'H' and resid 63 through 82 Processing helix chain 'H' and resid 86 through 105 removed outlier: 4.012A pdb=" N LYS H 91 " --> pdb=" O SER H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 118 removed outlier: 4.913A pdb=" N THR H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N PHE H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 143 Processing helix chain 'H' and resid 161 through 170 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 213 through 221 Processing helix chain 'H' and resid 248 through 250 No H-bonds generated for 'chain 'H' and resid 248 through 250' 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 293 through 303 removed outlier: 3.701A pdb=" N VAL H 296 " --> pdb=" O PRO H 293 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER H 297 " --> pdb=" O SER H 294 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS H 302 " --> pdb=" O GLU H 299 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU H 303 " --> pdb=" O LEU H 300 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 45 Proline residue: I 39 - end of helix Processing helix chain 'I' and resid 63 through 67 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 114 through 123 removed outlier: 3.519A pdb=" N VAL I 117 " --> pdb=" O LEU I 114 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL I 118 " --> pdb=" O HIS I 115 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA I 123 " --> pdb=" O LEU I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 189 Processing helix chain 'I' and resid 209 through 217 Processing helix chain 'I' and resid 224 through 227 No H-bonds generated for 'chain 'I' and resid 224 through 227' Processing helix chain 'I' and resid 230 through 235 Processing helix chain 'I' and resid 282 through 291 removed outlier: 4.288A pdb=" N ARG I 286 " --> pdb=" O TRP I 282 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP I 290 " --> pdb=" O ARG I 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 45 Proline residue: J 39 - end of helix Processing helix chain 'J' and resid 63 through 67 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 114 through 123 removed outlier: 3.519A pdb=" N VAL J 117 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL J 118 " --> pdb=" O HIS J 115 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA J 123 " --> pdb=" O LEU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 189 Processing helix chain 'J' and resid 209 through 217 Processing helix chain 'J' and resid 224 through 227 No H-bonds generated for 'chain 'J' and resid 224 through 227' Processing helix chain 'J' and resid 230 through 235 Processing helix chain 'J' and resid 282 through 291 removed outlier: 4.288A pdb=" N ARG J 286 " --> pdb=" O TRP J 282 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP J 290 " --> pdb=" O ARG J 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 60 No H-bonds generated for 'chain 'L' and resid 58 through 60' Processing helix chain 'L' and resid 91 through 118 Processing helix chain 'L' and resid 123 through 133 Processing helix chain 'L' and resid 135 through 140 Processing helix chain 'L' and resid 146 through 157 removed outlier: 3.790A pdb=" N SER L 157 " --> pdb=" O LYS L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 169 through 182 removed outlier: 4.095A pdb=" N GLU L 173 " --> pdb=" O GLU L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 203 through 216 Processing helix chain 'L' and resid 243 through 263 removed outlier: 3.832A pdb=" N SER L 248 " --> pdb=" O THR L 244 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 61 Processing helix chain 'S' and resid 138 through 147 removed outlier: 3.974A pdb=" N ASN S 147 " --> pdb=" O ALA S 143 " (cutoff:3.500A) Processing helix chain 'S' and resid 166 through 178 Processing helix chain 'S' and resid 196 through 215 removed outlier: 3.602A pdb=" N GLN S 212 " --> pdb=" O LEU S 208 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL S 215 " --> pdb=" O VAL S 211 " (cutoff:3.500A) Processing helix chain 'S' and resid 229 through 242 Processing helix chain 'd' and resid 4 through 15 Processing sheet with id= A, first strand: chain 'A' and resid 149 through 152 removed outlier: 6.783A pdb=" N GLU A 90 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU A 47 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N PHE A 92 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS A 95 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 155 through 157 Processing sheet with id= C, first strand: chain 'A' and resid 287 through 292 removed outlier: 5.750A pdb=" N MET A 181 " --> pdb=" O HIS A 288 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N HIS A 290 " --> pdb=" O MET A 181 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N MET A 183 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR A 292 " --> pdb=" O MET A 183 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N PHE A 185 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 239 through 241 removed outlier: 6.356A pdb=" N ASP A 206 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL A 212 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 373 through 375 Processing sheet with id= F, first strand: chain 'A' and resid 411 through 413 removed outlier: 6.983A pdb=" N SER A 429 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N SER A 447 " --> pdb=" O VAL A 430 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 149 through 152 removed outlier: 6.824A pdb=" N GLU B 90 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU B 47 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE B 92 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 155 through 157 Processing sheet with id= I, first strand: chain 'B' and resid 288 through 292 Processing sheet with id= J, first strand: chain 'B' and resid 239 through 241 Processing sheet with id= K, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.759A pdb=" N SER B 377 " --> pdb=" O LEU B 361 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 373 through 375 Processing sheet with id= M, first strand: chain 'B' and resid 429 through 431 removed outlier: 6.640A pdb=" N SER B 447 " --> pdb=" O VAL B 430 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.479A pdb=" N HIS C 188 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N THR C 167 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE C 190 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR C 215 " --> pdb=" O VAL C 191 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 232 through 234 removed outlier: 7.117A pdb=" N LEU C 323 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 245 through 248 Processing sheet with id= Q, first strand: chain 'D' and resid 164 through 168 removed outlier: 6.514A pdb=" N HIS D 188 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR D 167 " --> pdb=" O HIS D 188 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE D 190 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N THR D 215 " --> pdb=" O VAL D 191 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'D' and resid 232 through 234 removed outlier: 7.343A pdb=" N LEU D 323 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 245 through 248 Processing sheet with id= T, first strand: chain 'E' and resid 331 through 336 removed outlier: 3.600A pdb=" N ARG E 357 " --> pdb=" O ASP E 331 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL E 360 " --> pdb=" O PRO E 382 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER E 384 " --> pdb=" O VAL E 360 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ASP E 362 " --> pdb=" O SER E 384 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU E 386 " --> pdb=" O ASP E 362 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 400 through 404 removed outlier: 7.637A pdb=" N LEU E 403 " --> pdb=" O PRO E 433 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU E 435 " --> pdb=" O LEU E 403 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU E 499 " --> pdb=" O VAL E 436 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 405 through 408 removed outlier: 6.691A pdb=" N MET E 415 " --> pdb=" O HIS E 406 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 331 through 336 removed outlier: 7.802A pdb=" N VAL F 360 " --> pdb=" O PRO F 382 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N SER F 384 " --> pdb=" O VAL F 360 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ASP F 362 " --> pdb=" O SER F 384 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU F 386 " --> pdb=" O ASP F 362 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 401 through 404 removed outlier: 6.241A pdb=" N LEU F 499 " --> pdb=" O VAL F 436 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 414 through 417 removed outlier: 3.659A pdb=" N VAL F 414 " --> pdb=" O THR F 492 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 123 through 127 Processing sheet with id= AA, first strand: chain 'G' and resid 192 through 196 removed outlier: 7.493A pdb=" N VAL G 195 " --> pdb=" O PRO G 225 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR G 227 " --> pdb=" O VAL G 195 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU G 283 " --> pdb=" O VAL G 228 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 206 through 209 removed outlier: 3.613A pdb=" N ILE G 206 " --> pdb=" O THR G 276 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN G 208 " --> pdb=" O ASP G 274 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP G 274 " --> pdb=" O ASN G 208 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 123 through 127 Processing sheet with id= AD, first strand: chain 'H' and resid 192 through 196 removed outlier: 7.493A pdb=" N VAL H 195 " --> pdb=" O PRO H 225 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TYR H 227 " --> pdb=" O VAL H 195 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU H 283 " --> pdb=" O VAL H 228 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 206 through 209 removed outlier: 3.613A pdb=" N ILE H 206 " --> pdb=" O THR H 276 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN H 208 " --> pdb=" O ASP H 274 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP H 274 " --> pdb=" O ASN H 208 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'I' and resid 3 through 8 removed outlier: 6.708A pdb=" N ASP I 100 " --> pdb=" O GLN I 4 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL I 6 " --> pdb=" O ASP I 100 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU I 102 " --> pdb=" O VAL I 6 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N MET I 8 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU I 104 " --> pdb=" O MET I 8 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'I' and resid 51 through 54 removed outlier: 3.521A pdb=" N ILE I 78 " --> pdb=" O VAL I 53 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 128 through 133 Processing sheet with id= AI, first strand: chain 'I' and resid 193 through 196 removed outlier: 5.707A pdb=" N ASP I 161 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU I 167 " --> pdb=" O ASP I 161 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'J' and resid 3 through 8 removed outlier: 6.707A pdb=" N ASP J 100 " --> pdb=" O GLN J 4 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL J 6 " --> pdb=" O ASP J 100 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU J 102 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N MET J 8 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU J 104 " --> pdb=" O MET J 8 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'J' and resid 51 through 54 removed outlier: 3.520A pdb=" N ILE J 78 " --> pdb=" O VAL J 53 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'J' and resid 128 through 133 Processing sheet with id= AM, first strand: chain 'J' and resid 193 through 196 removed outlier: 5.706A pdb=" N ASP J 161 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU J 167 " --> pdb=" O ASP J 161 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'L' and resid 41 through 46 removed outlier: 3.925A pdb=" N ILE L 41 " --> pdb=" O LEU L 35 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N SER L 34 " --> pdb=" O VAL L 23 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL L 23 " --> pdb=" O SER L 34 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP L 83 " --> pdb=" O ILE L 73 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL L 75 " --> pdb=" O TYR L 81 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR L 81 " --> pdb=" O VAL L 75 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'L' and resid 224 through 227 Processing sheet with id= AP, first strand: chain 'S' and resid 42 through 46 removed outlier: 4.770A pdb=" N CYS S 135 " --> pdb=" O THR S 46 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY S 82 " --> pdb=" O ASP S 134 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'S' and resid 155 through 159 Processing sheet with id= AR, first strand: chain 'S' and resid 256 through 258 Processing sheet with id= AS, first strand: chain 'S' and resid 293 through 295 Processing sheet with id= AT, first strand: chain 'S' and resid 300 through 302 Processing sheet with id= AU, first strand: chain 'S' and resid 459 through 462 removed outlier: 6.767A pdb=" N GLU S 372 " --> pdb=" O ARG S 460 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLY S 462 " --> pdb=" O GLU S 370 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLU S 370 " --> pdb=" O GLY S 462 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA S 419 " --> pdb=" O LYS S 426 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL S 428 " --> pdb=" O VAL S 417 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL S 417 " --> pdb=" O VAL S 428 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'S' and resid 440 through 446 removed outlier: 5.591A pdb=" N ARG S 445 " --> pdb=" O LEU S 453 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU S 453 " --> pdb=" O ARG S 445 " (cutoff:3.500A) 1110 hydrogen bonds defined for protein. 3120 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: 9.88 Time building geometry restraints manager: 11.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4891 1.31 - 1.43: 6853 1.43 - 1.56: 17089 1.56 - 1.68: 6 1.68 - 1.81: 193 Bond restraints: 29032 Sorted by residual: bond pdb=" C16BC7B C 401 " pdb=" N08BC7B C 401 " ideal model delta sigma weight residual 1.341 1.463 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C16AC7B C 401 " pdb=" N08AC7B C 401 " ideal model delta sigma weight residual 1.341 1.463 -0.122 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C15AC7B C 401 " pdb=" N07AC7B C 401 " ideal model delta sigma weight residual 1.341 1.454 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C15BC7B C 401 " pdb=" N07BC7B C 401 " ideal model delta sigma weight residual 1.341 1.453 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" CD2 TRP B 628 " pdb=" CE2 TRP B 628 " ideal model delta sigma weight residual 1.409 1.484 -0.075 1.70e-02 3.46e+03 1.94e+01 ... (remaining 29027 not shown) Histogram of bond angle deviations from ideal: 98.72 - 106.12: 658 106.12 - 113.52: 16632 113.52 - 120.92: 12788 120.92 - 128.32: 9212 128.32 - 135.72: 175 Bond angle restraints: 39465 Sorted by residual: angle pdb=" CD2 TRP A 317 " pdb=" CE3 TRP A 317 " pdb=" CZ3 TRP A 317 " ideal model delta sigma weight residual 118.60 129.45 -10.85 1.30e+00 5.92e-01 6.97e+01 angle pdb=" CD2 TRP A 397 " pdb=" CE3 TRP A 397 " pdb=" CZ3 TRP A 397 " ideal model delta sigma weight residual 118.60 129.44 -10.84 1.30e+00 5.92e-01 6.95e+01 angle pdb=" CD2 TRP F 476 " pdb=" CE3 TRP F 476 " pdb=" CZ3 TRP F 476 " ideal model delta sigma weight residual 118.60 129.43 -10.83 1.30e+00 5.92e-01 6.94e+01 angle pdb=" CD2 TRP L 135 " pdb=" CE3 TRP L 135 " pdb=" CZ3 TRP L 135 " ideal model delta sigma weight residual 118.60 129.42 -10.82 1.30e+00 5.92e-01 6.92e+01 angle pdb=" CD2 TRP F 350 " pdb=" CE3 TRP F 350 " pdb=" CZ3 TRP F 350 " ideal model delta sigma weight residual 118.60 129.42 -10.82 1.30e+00 5.92e-01 6.92e+01 ... (remaining 39460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.64: 17032 29.64 - 59.28: 306 59.28 - 88.91: 30 88.91 - 118.55: 4 118.55 - 148.19: 2 Dihedral angle restraints: 17374 sinusoidal: 5502 harmonic: 11872 Sorted by residual: dihedral pdb=" CA ILE F 198 " pdb=" C ILE F 198 " pdb=" N PRO F 199 " pdb=" CA PRO F 199 " ideal model delta harmonic sigma weight residual 180.00 154.18 25.82 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ILE E 198 " pdb=" C ILE E 198 " pdb=" N PRO E 199 " pdb=" CA PRO E 199 " ideal model delta harmonic sigma weight residual 180.00 155.10 24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ASN D 242 " pdb=" C ASN D 242 " pdb=" N GLY D 243 " pdb=" CA GLY D 243 " ideal model delta harmonic sigma weight residual -180.00 -155.22 -24.78 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 17371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.017: 4864 1.017 - 2.034: 0 2.034 - 3.050: 0 3.050 - 4.067: 0 4.067 - 5.084: 4 Chirality restraints: 4868 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 -2.61 5.08 2.00e-01 2.50e+01 6.46e+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 -2.61 5.08 2.00e-01 2.50e+01 6.44e+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 -2.43 4.90 2.00e-01 2.50e+01 6.01e+02 ... (remaining 4865 not shown) Planarity restraints: 5057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 395 " 0.050 5.00e-02 4.00e+02 7.45e-02 8.87e+00 pdb=" N PRO F 396 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO F 396 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 396 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 395 " -0.048 5.00e-02 4.00e+02 7.28e-02 8.48e+00 pdb=" N PRO E 396 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 396 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 396 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR H 292 " -0.044 5.00e-02 4.00e+02 6.60e-02 6.98e+00 pdb=" N PRO H 293 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO H 293 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 293 " -0.037 5.00e-02 4.00e+02 ... (remaining 5054 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4923 2.77 - 3.30: 25655 3.30 - 3.84: 47666 3.84 - 4.37: 52471 4.37 - 4.90: 92441 Nonbonded interactions: 223156 Sorted by model distance: nonbonded pdb=" OG SER D 30 " pdb=" OE1 GLU D 33 " model vdw 2.239 2.440 nonbonded pdb=" O LEU H 73 " pdb=" OG SER H 77 " model vdw 2.253 2.440 nonbonded pdb=" O LEU G 73 " pdb=" OG SER G 77 " model vdw 2.253 2.440 nonbonded pdb=" OG SER B 130 " pdb=" O GLN B 267 " model vdw 2.273 2.440 nonbonded pdb=" O SER D 17 " pdb=" OG1 THR D 21 " model vdw 2.312 2.440 ... (remaining 223151 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 'C' and resid 8 through 351) selection = (chain 'D' and (resid 8 through 98 or resid 126 through 351)) } 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: 6.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 25.400 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 69.520 Find NCS groups from input model: 1.420 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 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 : 0.005 0.122 29032 Z= 0.344 Angle : 0.871 17.417 39465 Z= 0.509 Chirality : 0.153 5.084 4868 Planarity : 0.006 0.074 5057 Dihedral : 12.435 148.190 9588 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: -3.78 (0.11), residues: 4046 helix: -2.57 (0.09), residues: 1587 sheet: -2.25 (0.20), residues: 575 loop : -2.44 (0.13), residues: 1884 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 860 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 3 residues processed: 878 average time/residue: 0.3620 time to fit residues: 523.4455 Evaluate side-chains 525 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 522 time to evaluate : 3.220 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2397 time to fit residues: 5.8794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 342 optimal weight: 6.9990 chunk 307 optimal weight: 30.0000 chunk 170 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 207 optimal weight: 0.4980 chunk 164 optimal weight: 0.9980 chunk 318 optimal weight: 0.4980 chunk 123 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 236 optimal weight: 8.9990 chunk 368 optimal weight: 40.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 HIS B 63 GLN B 72 ASN C 154 GLN C 252 HIS C 261 HIS D 138 ASN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 GLN F 479 HIS H 13 GLN J 190 HIS L 40 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 29032 Z= 0.233 Angle : 0.603 9.833 39465 Z= 0.325 Chirality : 0.045 0.178 4868 Planarity : 0.004 0.066 5057 Dihedral : 5.670 167.759 4102 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: -2.14 (0.12), residues: 4046 helix: -0.63 (0.12), residues: 1599 sheet: -1.92 (0.20), residues: 577 loop : -1.90 (0.13), residues: 1870 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 551 time to evaluate : 3.450 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 56 residues processed: 604 average time/residue: 0.3642 time to fit residues: 367.5759 Evaluate side-chains 526 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 470 time to evaluate : 3.440 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.2708 time to fit residues: 33.8410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 204 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 251 optimal weight: 0.4980 chunk 101 optimal weight: 0.1980 chunk 369 optimal weight: 20.0000 chunk 399 optimal weight: 20.0000 chunk 328 optimal weight: 4.9990 chunk 366 optimal weight: 40.0000 chunk 125 optimal weight: 6.9990 chunk 296 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 337 HIS B 214 HIS C 130 GLN D 188 HIS D 309 HIS D 345 HIS E 254 ASN E 347 GLN ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN F 194 GLN ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 477 GLN G 116 HIS H 116 HIS L 40 ASN L 67 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 29032 Z= 0.252 Angle : 0.648 15.171 39465 Z= 0.347 Chirality : 0.047 0.239 4868 Planarity : 0.004 0.057 5057 Dihedral : 5.627 172.079 4102 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: -1.02 (0.13), residues: 4046 helix: 0.53 (0.13), residues: 1597 sheet: -1.54 (0.20), residues: 594 loop : -1.41 (0.14), residues: 1855 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 517 time to evaluate : 3.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 31 residues processed: 565 average time/residue: 0.3716 time to fit residues: 349.1881 Evaluate side-chains 438 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 407 time to evaluate : 3.394 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2608 time to fit residues: 19.6613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 364 optimal weight: 30.0000 chunk 277 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 176 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 370 optimal weight: 20.0000 chunk 392 optimal weight: 30.0000 chunk 193 optimal weight: 0.5980 chunk 351 optimal weight: 8.9990 chunk 105 optimal weight: 0.5980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 GLN F 194 GLN F 238 GLN F 245 ASN F 430 HIS F 486 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.6914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 29032 Z= 0.309 Angle : 0.642 12.843 39465 Z= 0.349 Chirality : 0.048 0.227 4868 Planarity : 0.004 0.057 5057 Dihedral : 5.662 162.239 4102 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 2.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.13), residues: 4046 helix: 0.81 (0.13), residues: 1605 sheet: -1.47 (0.21), residues: 566 loop : -1.20 (0.14), residues: 1875 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 427 time to evaluate : 3.734 Fit side-chains outliers start: 75 outliers final: 37 residues processed: 474 average time/residue: 0.3813 time to fit residues: 298.0133 Evaluate side-chains 402 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 365 time to evaluate : 3.345 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2988 time to fit residues: 25.1196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 326 optimal weight: 0.0670 chunk 222 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 292 optimal weight: 6.9990 chunk 161 optimal weight: 0.7980 chunk 334 optimal weight: 0.6980 chunk 271 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 200 optimal weight: 0.0970 chunk 352 optimal weight: 5.9990 chunk 99 optimal weight: 20.0000 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 234 GLN ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN F 254 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.7048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 29032 Z= 0.176 Angle : 0.545 13.293 39465 Z= 0.298 Chirality : 0.044 0.206 4868 Planarity : 0.003 0.055 5057 Dihedral : 5.434 167.613 4102 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 4046 helix: 1.32 (0.13), residues: 1609 sheet: -1.26 (0.22), residues: 589 loop : -0.99 (0.14), residues: 1848 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 393 time to evaluate : 3.391 Fit side-chains outliers start: 42 outliers final: 18 residues processed: 425 average time/residue: 0.3757 time to fit residues: 263.0742 Evaluate side-chains 377 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 359 time to evaluate : 3.551 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2672 time to fit residues: 13.5937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 132 optimal weight: 7.9990 chunk 353 optimal weight: 30.0000 chunk 77 optimal weight: 6.9990 chunk 230 optimal weight: 4.9990 chunk 96 optimal weight: 30.0000 chunk 392 optimal weight: 10.0000 chunk 326 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 ASN C 158 HIS C 349 HIS D 72 GLN ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN ** E 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 HIS ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 HIS ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.8575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.109 29032 Z= 0.570 Angle : 0.766 14.449 39465 Z= 0.409 Chirality : 0.052 0.211 4868 Planarity : 0.004 0.062 5057 Dihedral : 6.219 165.989 4102 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 4046 helix: 0.88 (0.13), residues: 1610 sheet: -1.48 (0.21), residues: 576 loop : -1.19 (0.14), residues: 1860 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 345 time to evaluate : 3.298 Fit side-chains outliers start: 47 outliers final: 20 residues processed: 383 average time/residue: 0.3886 time to fit residues: 246.7096 Evaluate side-chains 324 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 304 time to evaluate : 3.421 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 1 residues processed: 20 average time/residue: 0.3473 time to fit residues: 17.5163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 378 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 223 optimal weight: 0.8980 chunk 286 optimal weight: 0.7980 chunk 222 optimal weight: 0.7980 chunk 330 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 391 optimal weight: 20.0000 chunk 244 optimal weight: 0.4980 chunk 238 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 ASN ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.8561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 29032 Z= 0.217 Angle : 0.581 14.409 39465 Z= 0.314 Chirality : 0.045 0.175 4868 Planarity : 0.003 0.058 5057 Dihedral : 5.772 170.999 4102 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 4046 helix: 1.30 (0.13), residues: 1617 sheet: -1.31 (0.22), residues: 558 loop : -1.02 (0.14), residues: 1871 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 345 time to evaluate : 3.422 Fit side-chains outliers start: 33 outliers final: 19 residues processed: 367 average time/residue: 0.3874 time to fit residues: 236.1717 Evaluate side-chains 332 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 313 time to evaluate : 3.483 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 1 residues processed: 19 average time/residue: 0.3056 time to fit residues: 15.0313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 242 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 248 optimal weight: 0.7980 chunk 266 optimal weight: 6.9990 chunk 193 optimal weight: 0.0270 chunk 36 optimal weight: 4.9990 chunk 307 optimal weight: 20.0000 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.8656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 29032 Z= 0.221 Angle : 0.565 13.844 39465 Z= 0.307 Chirality : 0.044 0.200 4868 Planarity : 0.003 0.058 5057 Dihedral : 5.669 175.548 4102 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 4046 helix: 1.49 (0.13), residues: 1612 sheet: -1.26 (0.21), residues: 590 loop : -0.91 (0.15), residues: 1844 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 328 time to evaluate : 3.439 Fit side-chains outliers start: 21 outliers final: 9 residues processed: 345 average time/residue: 0.4016 time to fit residues: 229.7178 Evaluate side-chains 325 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 316 time to evaluate : 3.404 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.2984 time to fit residues: 9.4581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 355 optimal weight: 40.0000 chunk 374 optimal weight: 0.1980 chunk 342 optimal weight: 8.9990 chunk 364 optimal weight: 5.9990 chunk 219 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 286 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 329 optimal weight: 0.8980 chunk 344 optimal weight: 10.0000 chunk 363 optimal weight: 40.0000 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.8857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 29032 Z= 0.271 Angle : 0.583 15.576 39465 Z= 0.315 Chirality : 0.045 0.210 4868 Planarity : 0.003 0.058 5057 Dihedral : 5.713 175.673 4102 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 4046 helix: 1.48 (0.13), residues: 1616 sheet: -1.26 (0.22), residues: 571 loop : -0.91 (0.15), residues: 1859 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 321 time to evaluate : 3.681 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 331 average time/residue: 0.4169 time to fit residues: 225.9883 Evaluate side-chains 320 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 309 time to evaluate : 3.435 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.3002 time to fit residues: 10.5392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 239 optimal weight: 6.9990 chunk 385 optimal weight: 30.0000 chunk 235 optimal weight: 0.9980 chunk 182 optimal weight: 0.9980 chunk 268 optimal weight: 4.9990 chunk 404 optimal weight: 20.0000 chunk 372 optimal weight: 30.0000 chunk 322 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 197 optimal weight: 0.6980 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.9100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 29032 Z= 0.305 Angle : 0.609 15.377 39465 Z= 0.327 Chirality : 0.046 0.217 4868 Planarity : 0.003 0.058 5057 Dihedral : 5.783 176.552 4102 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 4046 helix: 1.50 (0.13), residues: 1607 sheet: -1.26 (0.22), residues: 569 loop : -0.92 (0.15), residues: 1870 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 316 time to evaluate : 3.190 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 326 average time/residue: 0.4015 time to fit residues: 214.5886 Evaluate side-chains 315 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 308 time to evaluate : 3.518 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.3013 time to fit residues: 8.4461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 255 optimal weight: 0.8980 chunk 343 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 296 optimal weight: 0.9990 chunk 47 optimal weight: 0.0980 chunk 89 optimal weight: 10.0000 chunk 322 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 331 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 59 optimal weight: 0.1980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.122950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.092562 restraints weight = 89571.635| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.71 r_work: 0.3224 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.9179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 29032 Z= 0.275 Angle : 0.594 15.394 39465 Z= 0.319 Chirality : 0.045 0.213 4868 Planarity : 0.003 0.058 5057 Dihedral : 5.762 178.480 4102 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 4046 helix: 1.50 (0.13), residues: 1618 sheet: -1.22 (0.22), residues: 569 loop : -0.87 (0.15), residues: 1859 =============================================================================== Job complete usr+sys time: 6797.72 seconds wall clock time: 123 minutes 28.96 seconds (7408.96 seconds total)