Starting phenix.real_space_refine (version: dev) on Mon Feb 27 06:55:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7var_31860/02_2023/7var_31860_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7var_31860/02_2023/7var_31860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7var_31860/02_2023/7var_31860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7var_31860/02_2023/7var_31860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7var_31860/02_2023/7var_31860_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7var_31860/02_2023/7var_31860_updated.pdb" } resolution = 2.9 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 53": "OE1" <-> "OE2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 296": "OE1" <-> "OE2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 29520 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4476 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4467 Classifications: {'peptide': 577} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain breaks: 1 Chain: "C" Number of atoms: 4476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4476 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 793 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 314 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 314 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 981 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.27, per 1000 atoms: 0.55 Number of scatterers: 29520 At special positions: 0 Unit cell: (140.8, 174.24, 150.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 103 16.00 P 5 15.00 Mg 2 11.99 O 5565 8.00 N 5125 7.00 C 18720 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: 13.07 Conformation dependent library (CDL) restraints added in 4.5 seconds 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6916 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 36 sheets defined 42.4% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.38 Creating SS restraints... Processing helix chain 'A' and resid 91 through 98 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 259 through 271 Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 296 through 315 removed outlier: 4.101A pdb=" N GLU A 300 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 341 Processing helix chain 'A' and resid 352 through 364 removed outlier: 4.004A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 363 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 447 through 471 removed outlier: 3.970A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 475 No H-bonds generated for 'chain 'A' and resid 473 through 475' Processing helix chain 'A' and resid 478 through 493 Processing helix chain 'A' and resid 509 through 532 Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.975A pdb=" N ARG A 552 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 574 removed outlier: 3.678A pdb=" N GLU A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 259 through 271 Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 296 through 315 removed outlier: 4.738A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 Processing helix chain 'B' and resid 354 through 364 removed outlier: 4.304A pdb=" N ARG B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 432 through 442 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 447 through 470 removed outlier: 3.783A pdb=" N GLN B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 493 Processing helix chain 'B' and resid 509 through 531 Processing helix chain 'B' and resid 536 through 541 removed outlier: 3.688A pdb=" N GLN B 541 " --> pdb=" O ASP B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.501A pdb=" N ARG B 550 " --> pdb=" O ARG B 547 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG B 552 " --> pdb=" O GLY B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 575 removed outlier: 3.612A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 259 through 271 removed outlier: 3.643A pdb=" N VAL C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 296 through 315 removed outlier: 3.885A pdb=" N GLU C 300 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 340 Processing helix chain 'C' and resid 354 through 364 removed outlier: 3.892A pdb=" N ARG C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 394 through 401 removed outlier: 3.690A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.523A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 442 Processing helix chain 'C' and resid 447 through 471 removed outlier: 4.164A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 475 No H-bonds generated for 'chain 'C' and resid 473 through 475' Processing helix chain 'C' and resid 478 through 493 Processing helix chain 'C' and resid 509 through 531 Processing helix chain 'C' and resid 536 through 540 Processing helix chain 'C' and resid 543 through 549 Processing helix chain 'C' and resid 551 through 553 No H-bonds generated for 'chain 'C' and resid 551 through 553' Processing helix chain 'C' and resid 556 through 577 Proline residue: C 560 - end of helix removed outlier: 3.749A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 213 through 216 Processing helix chain 'D' and resid 228 through 249 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 287 through 297 removed outlier: 4.504A pdb=" N ARG D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 362 through 365 No H-bonds generated for 'chain 'D' and resid 362 through 365' Processing helix chain 'D' and resid 375 through 399 removed outlier: 3.564A pdb=" N LYS D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 395 " --> pdb=" O ASP D 391 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 421 Processing helix chain 'D' and resid 432 through 445 removed outlier: 3.989A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 450 No H-bonds generated for 'chain 'D' and resid 448 through 450' Processing helix chain 'D' and resid 456 through 462 Processing helix chain 'D' and resid 470 through 472 No H-bonds generated for 'chain 'D' and resid 470 through 472' Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 136 through 141 removed outlier: 3.616A pdb=" N MET E 141 " --> pdb=" O THR E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 176 through 178 No H-bonds generated for 'chain 'E' and resid 176 through 178' Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'E' and resid 213 through 216 Processing helix chain 'E' and resid 228 through 249 removed outlier: 3.646A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 260 through 274 Processing helix chain 'E' and resid 285 through 297 removed outlier: 4.479A pdb=" N TYR E 288 " --> pdb=" O GLY E 285 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLU E 296 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG E 297 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 319 No H-bonds generated for 'chain 'E' and resid 317 through 319' Processing helix chain 'E' and resid 324 through 330 Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'E' and resid 362 through 365 No H-bonds generated for 'chain 'E' and resid 362 through 365' Processing helix chain 'E' and resid 375 through 399 removed outlier: 4.193A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 403 No H-bonds generated for 'chain 'E' and resid 401 through 403' Processing helix chain 'E' and resid 406 through 421 Processing helix chain 'E' and resid 432 through 443 Processing helix chain 'E' and resid 448 through 450 No H-bonds generated for 'chain 'E' and resid 448 through 450' Processing helix chain 'E' and resid 458 through 461 No H-bonds generated for 'chain 'E' and resid 458 through 461' Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.552A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY F 90 " --> pdb=" O GLU F 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 86 through 90' Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 160 through 170 Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 198 through 211 Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'F' and resid 229 through 249 removed outlier: 3.776A pdb=" N THR F 234 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.595A pdb=" N PHE F 247 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N HIS F 249 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 287 through 297 removed outlier: 3.734A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ARG F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'F' and resid 341 through 346 removed outlier: 3.512A pdb=" N LYS F 346 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 364 No H-bonds generated for 'chain 'F' and resid 362 through 364' Processing helix chain 'F' and resid 375 through 398 removed outlier: 3.527A pdb=" N LYS F 394 " --> pdb=" O VAL F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 403 No H-bonds generated for 'chain 'F' and resid 401 through 403' Processing helix chain 'F' and resid 406 through 421 Processing helix chain 'F' and resid 432 through 445 removed outlier: 3.891A pdb=" N MET F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 450 No H-bonds generated for 'chain 'F' and resid 448 through 450' Processing helix chain 'F' and resid 456 through 462 Processing helix chain 'F' and resid 467 through 470 No H-bonds generated for 'chain 'F' and resid 467 through 470' Processing helix chain 'G' and resid 8 through 70 removed outlier: 3.913A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 82 Processing helix chain 'G' and resid 111 through 114 Processing helix chain 'G' and resid 121 through 207 removed outlier: 3.582A pdb=" N ALA G 126 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER G 127 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 7 through 15 Processing helix chain 'H' and resid 26 through 39 Processing helix chain 'H' and resid 55 through 58 Processing helix chain 'H' and resid 77 through 80 No H-bonds generated for 'chain 'H' and resid 77 through 80' Processing helix chain 'H' and resid 86 through 98 Processing helix chain 'I' and resid 84 through 118 removed outlier: 3.828A pdb=" N TYR I 88 " --> pdb=" O LEU I 84 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASP I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLU I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA I 110 " --> pdb=" O ARG I 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 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 100 through 114 Processing helix chain 'J' and resid 125 through 130 Proline residue: J 129 - end of helix No H-bonds generated for 'chain 'J' and resid 125 through 130' Processing helix chain 'J' and resid 132 through 138 Processing helix chain 'J' and resid 167 through 186 removed outlier: 4.523A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 118 removed outlier: 4.472A pdb=" N LEU K 85 " --> pdb=" O GLU K 82 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA K 86 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG K 87 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA K 105 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG K 106 " --> pdb=" O ALA K 103 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU K 107 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ASP K 108 " --> pdb=" O ALA K 105 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS K 116 " --> pdb=" O LEU K 113 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL K 118 " --> pdb=" O LEU K 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 92 Processing helix chain 'L' and resid 94 through 96 No H-bonds generated for 'chain 'L' and resid 94 through 96' Processing helix chain 'L' and resid 100 through 114 Processing helix chain 'L' and resid 125 through 138 Proline residue: L 129 - end of helix removed outlier: 4.715A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 187 removed outlier: 4.578A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 removed outlier: 6.456A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ILE A 6 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 75 Processing sheet with id= C, first strand: chain 'A' and resid 117 through 119 removed outlier: 3.555A pdb=" N GLY A 164 " --> pdb=" O TRP A 119 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 197 through 199 removed outlier: 3.740A pdb=" N ARG A 197 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS A 367 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL A 249 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N MET A 323 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 251 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 223 through 227 removed outlier: 6.562A pdb=" N ILE A 380 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ILE A 226 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY A 382 " --> pdb=" O ILE A 226 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 134 through 140 removed outlier: 6.735A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 157 through 160 removed outlier: 7.046A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 2 through 5 removed outlier: 4.343A pdb=" N ILE B 2 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ILE B 6 " --> pdb=" O LYS B 17 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 72 through 76 Processing sheet with id= J, first strand: chain 'B' and resid 117 through 119 removed outlier: 3.624A pdb=" N GLY B 164 " --> pdb=" O TRP B 119 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 405 through 407 removed outlier: 8.748A pdb=" N ALA B 224 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE B 380 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ILE B 226 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY B 382 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 249 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N MET B 323 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL B 251 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 366 through 369 Processing sheet with id= M, first strand: chain 'B' and resid 134 through 140 removed outlier: 6.520A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 157 through 160 removed outlier: 7.011A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 3 through 5 removed outlier: 6.642A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE C 6 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 72 through 75 Processing sheet with id= Q, first strand: chain 'C' and resid 117 through 119 Processing sheet with id= R, first strand: chain 'C' and resid 223 through 227 removed outlier: 8.576A pdb=" N ALA C 224 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE C 380 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE C 226 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLY C 382 " --> pdb=" O ILE C 226 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL C 249 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N MET C 323 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL C 251 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 366 through 369 Processing sheet with id= T, first strand: chain 'C' and resid 134 through 140 removed outlier: 6.663A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE C 143 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.828A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 11 through 15 removed outlier: 6.445A pdb=" N PHE D 20 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE D 14 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ASP D 34 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LEU D 75 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS D 36 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL D 73 " --> pdb=" O LYS D 36 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.621A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.950A pdb=" N ARG D 91 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ASN D 222 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA D 193 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N HIS D 252 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL D 190 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU D 254 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ALA D 192 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE D 256 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N MET D 194 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE D 311 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 336 through 338 Processing sheet with id= Z, first strand: chain 'E' and resid 11 through 15 removed outlier: 6.601A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU E 77 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL E 73 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.384A pdb=" N PHE E 93 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU E 219 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N VAL E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N HIS E 252 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL E 190 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU E 254 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA E 192 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE E 256 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE E 311 " --> pdb=" O LEU E 257 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'E' and resid 336 through 338 Processing sheet with id= AC, first strand: chain 'F' and resid 11 through 15 removed outlier: 6.564A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ASP F 34 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU F 75 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LYS F 36 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL F 73 " --> pdb=" O LYS F 36 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.688A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.971A pdb=" N PHE F 93 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU F 219 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE F 311 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 336 through 338 Processing sheet with id= AG, first strand: chain 'G' and resid 89 through 96 Processing sheet with id= AH, first strand: chain 'H' and resid 19 through 22 Processing sheet with id= AI, first strand: chain 'J' and resid 141 through 144 removed outlier: 3.748A pdb=" N GLU J 141 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL J 155 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU J 121 " --> pdb=" O ARG J 153 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG J 153 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 141 through 144 removed outlier: 3.595A pdb=" N ALA L 120 " --> pdb=" O VAL L 155 " (cutoff:3.500A) 1204 hydrogen bonds defined for protein. 3138 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: 11.55 Time building geometry restraints manager: 13.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9966 1.34 - 1.46: 5196 1.46 - 1.58: 14709 1.58 - 1.69: 9 1.69 - 1.81: 194 Bond restraints: 30074 Sorted by residual: bond pdb=" C4 ADP A 601 " pdb=" C5 ADP A 601 " ideal model delta sigma weight residual 1.490 1.385 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C5 ADP A 601 " pdb=" C6 ADP A 601 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" O1B ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 1.510 1.590 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" N ARG F 372 " pdb=" CA ARG F 372 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.87e+00 bond pdb=" N GLU D 296 " pdb=" CA GLU D 296 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.30e-02 5.92e+03 8.14e+00 ... (remaining 30069 not shown) Histogram of bond angle deviations from ideal: 100.06 - 108.00: 1258 108.00 - 115.94: 18470 115.94 - 123.87: 20299 123.87 - 131.81: 685 131.81 - 139.75: 42 Bond angle restraints: 40754 Sorted by residual: angle pdb=" PA ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 120.50 136.72 -16.22 3.00e+00 1.11e-01 2.92e+01 angle pdb=" O1B ADP A 601 " pdb=" PB ADP A 601 " pdb=" O2B ADP A 601 " ideal model delta sigma weight residual 119.90 106.99 12.91 3.00e+00 1.11e-01 1.85e+01 angle pdb=" N THR G 119 " pdb=" CA THR G 119 " pdb=" C THR G 119 " ideal model delta sigma weight residual 109.81 117.95 -8.14 2.21e+00 2.05e-01 1.36e+01 angle pdb=" CA ALA D 298 " pdb=" C ALA D 298 " pdb=" O ALA D 298 " ideal model delta sigma weight residual 121.56 117.98 3.58 1.09e+00 8.42e-01 1.08e+01 angle pdb=" C ALA E 441 " pdb=" N LEU E 442 " pdb=" CA LEU E 442 " ideal model delta sigma weight residual 122.06 116.03 6.03 1.86e+00 2.89e-01 1.05e+01 ... (remaining 40749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.89: 17738 27.89 - 55.78: 497 55.78 - 83.67: 71 83.67 - 111.56: 10 111.56 - 139.45: 2 Dihedral angle restraints: 18318 sinusoidal: 7500 harmonic: 10818 Sorted by residual: dihedral pdb=" O2A ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PA ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 79.45 -139.45 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 78.40 -138.41 1 2.00e+01 2.50e-03 4.19e+01 dihedral pdb=" C THR F 371 " pdb=" N THR F 371 " pdb=" CA THR F 371 " pdb=" CB THR F 371 " ideal model delta harmonic sigma weight residual -122.00 -137.73 15.73 0 2.50e+00 1.60e-01 3.96e+01 ... (remaining 18315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 4331 0.095 - 0.191: 235 0.191 - 0.286: 0 0.286 - 0.381: 0 0.381 - 0.477: 1 Chirality restraints: 4567 Sorted by residual: chirality pdb=" CA THR F 371 " pdb=" N THR F 371 " pdb=" C THR F 371 " pdb=" CB THR F 371 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" C2' ADP A 601 " pdb=" C1' ADP A 601 " pdb=" C3' ADP A 601 " pdb=" O2' ADP A 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.17 2.00e-01 2.50e+01 7.45e-01 chirality pdb=" CB ILE C 226 " pdb=" CA ILE C 226 " pdb=" CG1 ILE C 226 " pdb=" CG2 ILE C 226 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 4564 not shown) Planarity restraints: 5336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN L 124 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO L 125 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO L 125 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO L 125 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 101 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO G 102 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO G 102 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 102 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO E 324 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " -0.023 5.00e-02 4.00e+02 ... (remaining 5333 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 168 2.61 - 3.18: 25203 3.18 - 3.76: 44611 3.76 - 4.33: 63399 4.33 - 4.90: 106632 Nonbonded interactions: 240013 Sorted by model distance: nonbonded pdb=" OG SER C 235 " pdb="MG MG C 602 " model vdw 2.038 2.170 nonbonded pdb=" O1G ATP C 601 " pdb="MG MG C 602 " model vdw 2.065 2.170 nonbonded pdb=" OG SER H 25 " pdb=" OE1 GLU H 28 " model vdw 2.145 2.440 nonbonded pdb=" OD1 ASP F 34 " pdb=" OG SER F 74 " model vdw 2.216 2.440 nonbonded pdb=" OH TYR D 263 " pdb=" OD2 ASP D 290 " model vdw 2.228 2.440 ... (remaining 240008 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 32 or resid 34 through 578)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 32 or resid 34 through 578)) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 2 5.21 5 S 103 5.16 5 C 18720 2.51 5 N 5125 2.21 5 O 5565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 3.650 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: 17.500 Check model and map are aligned: 0.460 Process input model: 76.820 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.280 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:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 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 : 0.003 0.105 30074 Z= 0.183 Angle : 0.556 16.222 40754 Z= 0.308 Chirality : 0.043 0.477 4567 Planarity : 0.004 0.059 5336 Dihedral : 13.207 139.447 11402 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.80 % 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: 1.46 (0.14), residues: 3761 helix: 1.89 (0.14), residues: 1554 sheet: 0.35 (0.22), residues: 579 loop : 0.42 (0.16), residues: 1628 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 507 time to evaluate : 3.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 509 average time/residue: 1.9486 time to fit residues: 1117.3436 Evaluate side-chains 272 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 271 time to evaluate : 3.414 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 4.8409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 4.9990 chunk 282 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 292 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 217 optimal weight: 20.0000 chunk 338 optimal weight: 0.5980 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS A 541 GLN A 571 GLN B 202 ASN B 260 ASN B 423 ASN C 238 GLN F 206 GLN G 68 GLN G 181 GLN L 165 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.057 30074 Z= 0.387 Angle : 0.632 9.374 40754 Z= 0.327 Chirality : 0.048 0.187 4567 Planarity : 0.006 0.058 5336 Dihedral : 5.911 143.942 4199 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.80 (0.14), residues: 3761 helix: 1.14 (0.13), residues: 1542 sheet: 0.25 (0.21), residues: 558 loop : 0.21 (0.15), residues: 1661 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 274 time to evaluate : 3.587 Fit side-chains revert: symmetry clash outliers start: 77 outliers final: 18 residues processed: 331 average time/residue: 1.9508 time to fit residues: 733.9670 Evaluate side-chains 273 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 255 time to evaluate : 3.601 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 11 residues processed: 7 average time/residue: 0.5466 time to fit residues: 10.3330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 281 optimal weight: 0.4980 chunk 230 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 339 optimal weight: 7.9990 chunk 366 optimal weight: 9.9990 chunk 302 optimal weight: 2.9990 chunk 336 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 272 optimal weight: 4.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A 571 GLN B 477 GLN D 364 ASN F 310 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN G 180 GLN ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 30074 Z= 0.292 Angle : 0.563 11.480 40754 Z= 0.289 Chirality : 0.045 0.171 4567 Planarity : 0.005 0.050 5336 Dihedral : 5.831 150.829 4199 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.66 (0.14), residues: 3761 helix: 1.03 (0.14), residues: 1547 sheet: 0.10 (0.21), residues: 588 loop : 0.15 (0.15), residues: 1626 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 272 time to evaluate : 3.363 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 30 residues processed: 316 average time/residue: 1.8781 time to fit residues: 675.6456 Evaluate side-chains 270 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 240 time to evaluate : 3.449 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 22 residues processed: 8 average time/residue: 0.9726 time to fit residues: 14.5214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 7.9990 chunk 255 optimal weight: 9.9990 chunk 176 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 161 optimal weight: 0.0040 chunk 227 optimal weight: 0.0170 chunk 340 optimal weight: 9.9990 chunk 360 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 chunk 322 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 overall best weight: 2.1634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A 571 GLN L 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 30074 Z= 0.212 Angle : 0.514 9.263 40754 Z= 0.263 Chirality : 0.043 0.172 4567 Planarity : 0.005 0.046 5336 Dihedral : 5.668 152.934 4199 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.74 (0.14), residues: 3761 helix: 1.07 (0.14), residues: 1556 sheet: 0.15 (0.22), residues: 568 loop : 0.20 (0.15), residues: 1637 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 260 time to evaluate : 3.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 31 residues processed: 309 average time/residue: 1.8442 time to fit residues: 655.6748 Evaluate side-chains 271 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 240 time to evaluate : 3.609 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 26 residues processed: 5 average time/residue: 0.3802 time to fit residues: 8.0393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 268 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 307 optimal weight: 5.9990 chunk 249 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 184 optimal weight: 10.0000 chunk 323 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A 571 GLN E 58 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.066 30074 Z= 0.474 Angle : 0.658 9.852 40754 Z= 0.338 Chirality : 0.049 0.183 4567 Planarity : 0.006 0.058 5336 Dihedral : 6.196 161.478 4199 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 2.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.28 (0.14), residues: 3761 helix: 0.70 (0.13), residues: 1541 sheet: -0.02 (0.21), residues: 591 loop : -0.07 (0.15), residues: 1629 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 253 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 49 residues processed: 329 average time/residue: 1.8204 time to fit residues: 702.1499 Evaluate side-chains 291 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 242 time to evaluate : 3.653 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 40 residues processed: 9 average time/residue: 0.5692 time to fit residues: 12.7485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 4.9990 chunk 324 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 360 optimal weight: 6.9990 chunk 299 optimal weight: 0.7980 chunk 167 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A 571 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 30074 Z= 0.239 Angle : 0.539 11.083 40754 Z= 0.276 Chirality : 0.044 0.161 4567 Planarity : 0.005 0.051 5336 Dihedral : 5.870 160.725 4199 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.49 (0.14), residues: 3761 helix: 0.93 (0.14), residues: 1545 sheet: 0.03 (0.21), residues: 600 loop : -0.00 (0.15), residues: 1616 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 252 time to evaluate : 3.745 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 47 residues processed: 321 average time/residue: 1.7821 time to fit residues: 662.5618 Evaluate side-chains 289 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 242 time to evaluate : 4.932 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 40 residues processed: 7 average time/residue: 0.5098 time to fit residues: 12.0053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 205 optimal weight: 0.3980 chunk 263 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 303 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 359 optimal weight: 9.9990 chunk 224 optimal weight: 10.0000 chunk 219 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A 571 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 ASN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 30074 Z= 0.237 Angle : 0.536 10.003 40754 Z= 0.273 Chirality : 0.044 0.158 4567 Planarity : 0.005 0.056 5336 Dihedral : 5.769 160.878 4199 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 2.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.57 (0.14), residues: 3761 helix: 1.02 (0.14), residues: 1546 sheet: 0.04 (0.21), residues: 597 loop : 0.04 (0.15), residues: 1618 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 252 time to evaluate : 3.698 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 49 residues processed: 316 average time/residue: 1.7448 time to fit residues: 639.5271 Evaluate side-chains 286 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 237 time to evaluate : 3.741 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 43 residues processed: 6 average time/residue: 0.6829 time to fit residues: 10.8236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 69 optimal weight: 0.0040 chunk 228 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 282 optimal weight: 2.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 30074 Z= 0.203 Angle : 0.522 11.402 40754 Z= 0.265 Chirality : 0.043 0.157 4567 Planarity : 0.005 0.048 5336 Dihedral : 5.657 162.415 4199 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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 (0.14), residues: 3761 helix: 1.14 (0.14), residues: 1531 sheet: 0.09 (0.21), residues: 577 loop : 0.07 (0.15), residues: 1653 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 248 time to evaluate : 3.760 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 47 residues processed: 306 average time/residue: 1.7212 time to fit residues: 609.2746 Evaluate side-chains 291 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 244 time to evaluate : 3.677 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 42 residues processed: 5 average time/residue: 0.5277 time to fit residues: 8.5033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 0.6980 chunk 344 optimal weight: 20.0000 chunk 314 optimal weight: 6.9990 chunk 335 optimal weight: 30.0000 chunk 201 optimal weight: 0.9980 chunk 145 optimal weight: 7.9990 chunk 263 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 302 optimal weight: 7.9990 chunk 316 optimal weight: 20.0000 chunk 333 optimal weight: 20.0000 overall best weight: 3.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN G 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 30074 Z= 0.294 Angle : 0.569 13.971 40754 Z= 0.289 Chirality : 0.045 0.162 4567 Planarity : 0.005 0.053 5336 Dihedral : 5.814 165.118 4199 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.54 (0.14), residues: 3761 helix: 1.00 (0.14), residues: 1547 sheet: 0.01 (0.21), residues: 596 loop : 0.01 (0.15), residues: 1618 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 251 time to evaluate : 3.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 54 residues processed: 310 average time/residue: 1.7849 time to fit residues: 643.6329 Evaluate side-chains 294 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 240 time to evaluate : 3.591 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 47 residues processed: 7 average time/residue: 0.7388 time to fit residues: 12.3519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 1.9990 chunk 354 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 168 optimal weight: 8.9990 chunk 246 optimal weight: 0.9990 chunk 371 optimal weight: 10.0000 chunk 342 optimal weight: 5.9990 chunk 295 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 228 optimal weight: 0.9990 chunk 181 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 541 GLN D 206 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN L 165 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 30074 Z= 0.147 Angle : 0.495 11.099 40754 Z= 0.251 Chirality : 0.042 0.167 4567 Planarity : 0.004 0.044 5336 Dihedral : 5.458 170.331 4199 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.86 (0.14), residues: 3761 helix: 1.30 (0.14), residues: 1534 sheet: 0.18 (0.22), residues: 547 loop : 0.15 (0.15), residues: 1680 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 255 time to evaluate : 3.667 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 44 residues processed: 305 average time/residue: 1.6705 time to fit residues: 591.2456 Evaluate side-chains 282 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 238 time to evaluate : 3.389 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 43 residues processed: 1 average time/residue: 0.2557 time to fit residues: 5.0614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 5.9990 chunk 315 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 296 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 304 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 541 GLN A 571 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN ** L 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.119211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.086780 restraints weight = 44544.531| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.82 r_work: 0.2926 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 30074 Z= 0.310 Angle : 0.580 9.554 40754 Z= 0.295 Chirality : 0.045 0.163 4567 Planarity : 0.005 0.056 5336 Dihedral : 5.809 177.830 4199 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.60 (0.14), residues: 3761 helix: 1.05 (0.14), residues: 1542 sheet: 0.04 (0.21), residues: 617 loop : 0.05 (0.16), residues: 1602 =============================================================================== Job complete usr+sys time: 10656.93 seconds wall clock time: 190 minutes 23.21 seconds (11423.21 seconds total)