Starting phenix.real_space_refine on Wed Feb 21 03:49:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxx_34364/02_2024/8gxx_34364_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxx_34364/02_2024/8gxx_34364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxx_34364/02_2024/8gxx_34364.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxx_34364/02_2024/8gxx_34364.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxx_34364/02_2024/8gxx_34364_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gxx_34364/02_2024/8gxx_34364_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 2 5.21 5 S 103 5.16 5 C 18735 2.51 5 N 5131 2.21 5 O 5574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29553 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} 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: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} 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: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} 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: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 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: 15.78, per 1000 atoms: 0.53 Number of scatterers: 29553 At special positions: 0 Unit cell: (148.57, 148.57, 176.79, 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 8 15.00 Mg 2 11.99 O 5574 8.00 N 5131 7.00 C 18735 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: 12.31 Conformation dependent library (CDL) restraints added in 5.5 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 138 helices and 37 sheets defined 42.8% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.40 Creating SS restraints... Processing helix chain 'A' and resid 91 through 97 removed outlier: 3.593A pdb=" N GLU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 260 through 268 removed outlier: 3.890A pdb=" N VAL A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 296 through 315 removed outlier: 4.046A 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 354 through 364 removed outlier: 3.627A pdb=" N ARG A 364 " --> 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 removed outlier: 3.656A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 432 through 442 Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 447 through 471 removed outlier: 3.683A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.667A 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 removed outlier: 3.757A pdb=" N GLN A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.537A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ARG A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N TYR A 553 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 577 Proline residue: A 560 - end of helix removed outlier: 4.222A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS A 575 " --> pdb=" O GLN A 571 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 577 " --> pdb=" O ALA A 573 " (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 removed outlier: 3.534A pdb=" N VAL B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) 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: 4.750A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.872A 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: 4.495A 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 436 through 442 Processing helix chain 'B' and resid 447 through 470 removed outlier: 4.476A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 478 through 494 Processing helix chain 'B' and resid 509 through 532 Processing helix chain 'B' and resid 536 through 541 removed outlier: 3.513A pdb=" N GLN B 541 " --> pdb=" O GLU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 552 removed outlier: 4.422A pdb=" N ARG B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 575 Proline residue: B 560 - end of helix removed outlier: 4.386A pdb=" N GLU B 564 " --> pdb=" O PRO B 560 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 260 through 271 removed outlier: 3.889A 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 297 through 315 removed outlier: 3.744A pdb=" N TYR C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 Processing helix chain 'C' and resid 354 through 364 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: 3.518A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 432 through 442 Proline residue: C 437 - end of helix Processing helix chain 'C' and resid 447 through 471 removed outlier: 3.979A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.320A 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 532 Processing helix chain 'C' and resid 536 through 541 Processing helix chain 'C' and resid 545 through 553 removed outlier: 4.650A pdb=" N ARG C 552 " --> pdb=" O ILE C 548 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TYR C 553 " --> pdb=" O GLY C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 577 Proline residue: C 560 - end of helix removed outlier: 3.572A pdb=" N LYS C 568 " --> pdb=" O GLU C 564 " (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 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' 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 248 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: 4.522A 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 360 through 365 removed outlier: 4.416A pdb=" N ASN D 363 " --> pdb=" O ARG D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 399 removed outlier: 3.834A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.137A 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: 4.077A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 462 Processing helix chain 'D' and resid 467 through 471 removed outlier: 3.567A pdb=" N TRP D 471 " --> pdb=" O GLU D 468 " (cutoff:3.500A) 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 121 through 123 No H-bonds generated for 'chain 'E' and resid 121 through 123' Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 175 through 178 No H-bonds generated for 'chain 'E' and resid 175 through 178' Processing helix chain 'E' and resid 198 through 211 Processing helix chain 'E' and resid 213 through 216 Processing helix chain 'E' and resid 228 through 249 removed outlier: 3.653A 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 removed outlier: 3.697A pdb=" N ARG E 274 " --> pdb=" O ILE E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 297 removed outlier: 4.483A pdb=" N ARG E 297 " --> pdb=" O THR E 293 " (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 332 Processing helix chain 'E' and resid 341 through 346 Processing helix chain 'E' and resid 360 through 364 removed outlier: 4.392A pdb=" N ASN E 363 " --> pdb=" O ARG E 360 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN E 364 " --> pdb=" O LEU E 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 360 through 364' Processing helix chain 'E' and resid 375 through 399 removed outlier: 4.521A pdb=" N ALA E 397 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 421 removed outlier: 4.164A pdb=" N ARG E 410 " --> pdb=" O GLU E 406 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TYR E 411 " --> pdb=" O ASN E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 445 removed outlier: 3.818A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) 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 456 through 462 Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' 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 210 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: 3.613A pdb=" N THR F 234 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.513A pdb=" N PHE F 247 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 4.319A 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 280 through 282 No H-bonds generated for 'chain 'F' and resid 280 through 282' Processing helix chain 'F' and resid 285 through 297 removed outlier: 4.067A pdb=" N TYR F 288 " --> pdb=" O GLY F 285 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU F 296 " --> pdb=" O THR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'F' and resid 341 through 345 Processing helix chain 'F' and resid 362 through 365 No H-bonds generated for 'chain 'F' and resid 362 through 365' Processing helix chain 'F' and resid 375 through 399 removed outlier: 3.727A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (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: 3.894A 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 'G' and resid 8 through 70 removed outlier: 3.736A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 82 Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 123 through 166 Processing helix chain 'G' and resid 168 through 208 Processing helix chain 'H' and resid 7 through 15 removed outlier: 3.989A pdb=" N ARG H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 38 Processing helix chain 'H' and resid 55 through 58 No H-bonds generated for 'chain 'H' and resid 55 through 58' Processing helix chain 'H' and resid 60 through 63 No H-bonds generated for 'chain 'H' and resid 60 through 63' Processing helix chain 'H' and resid 77 through 82 Processing helix chain 'H' and resid 86 through 98 Processing helix chain 'I' and resid 82 through 104 Processing helix chain 'I' and resid 107 through 118 Processing helix chain 'J' and resid 63 through 96 Proline residue: J 95 - end of helix Processing helix chain 'J' and resid 100 through 114 Processing helix chain 'J' and resid 125 through 138 Proline residue: J 129 - end of helix removed outlier: 5.175A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 186 removed outlier: 4.722A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 105 removed outlier: 3.524A pdb=" N ARG K 100 " --> pdb=" O ALA K 96 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 118 Processing helix chain 'L' and resid 63 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 98 through 114 Proline residue: L 101 - end of helix Processing helix chain 'L' and resid 125 through 130 Proline residue: L 129 - end of helix No H-bonds generated for 'chain 'L' and resid 125 through 130' Processing helix chain 'L' and resid 132 through 138 removed outlier: 3.695A pdb=" N ARG L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 186 removed outlier: 4.041A pdb=" N ARG L 173 " --> pdb=" O ALA L 169 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 2 through 5 removed outlier: 4.368A pdb=" N ILE A 2 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.765A 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 76 Processing sheet with id= C, first strand: chain 'A' and resid 82 through 84 removed outlier: 3.954A pdb=" N GLY A 82 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 250 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE A 288 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR A 252 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ASN A 290 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLY A 254 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 249 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ALA A 377 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU A 322 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N THR A 379 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA A 324 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A 381 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 117 through 119 Processing sheet with id= E, first strand: chain 'A' and resid 197 through 199 removed outlier: 4.558A pdb=" N LYS A 367 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 134 through 140 removed outlier: 6.745A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.849A 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: 6.788A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 3 through 5 removed outlier: 6.731A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.681A 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: 5.606A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.628A 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 75 Processing sheet with id= J, first strand: chain 'B' and resid 82 through 84 removed outlier: 3.980A pdb=" N GLY B 82 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 250 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE B 288 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR B 252 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA B 377 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU B 322 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR B 379 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ALA B 324 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 381 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B 384 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 164 through 166 removed outlier: 5.666A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.636A pdb=" N GLY B 155 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 197 through 199 removed outlier: 4.440A pdb=" N LYS B 367 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 157 through 160 removed outlier: 6.526A 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: 6.736A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.522A 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 76 Processing sheet with id= Q, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.222A pdb=" N GLY C 82 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ALA C 324 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL C 381 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 384 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 117 through 119 Processing sheet with id= S, first strand: chain 'C' and resid 366 through 369 removed outlier: 3.539A pdb=" N VAL C 378 " --> pdb=" O GLY C 366 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 134 through 139 removed outlier: 6.758A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 157 through 160 removed outlier: 6.594A 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: 6.237A pdb=" N PHE D 20 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE D 14 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ASP D 34 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU D 75 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS D 36 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.578A 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: 3.745A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 336 through 338 Processing sheet with id= Y, first strand: chain 'D' and resid 307 through 312 removed outlier: 3.588A pdb=" N LEU D 257 " --> pdb=" O ILE D 311 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 11 through 15 removed outlier: 6.632A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL E 73 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 81 through 84 Processing sheet with id= AB, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.859A pdb=" N ARG E 91 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N VAL E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N HIS E 252 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL E 190 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU E 254 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ALA E 192 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE E 256 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 336 through 338 Processing sheet with id= AD, first strand: chain 'F' and resid 11 through 15 removed outlier: 6.614A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ASP F 34 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU F 75 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LYS F 36 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL F 73 " --> pdb=" O LYS F 36 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 81 through 84 Processing sheet with id= AF, first strand: chain 'F' and resid 336 through 338 Processing sheet with id= AG, first strand: chain 'F' and resid 307 through 312 removed outlier: 3.760A pdb=" N LEU F 257 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA F 188 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE F 256 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL F 190 " --> pdb=" O ILE F 256 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 90 through 96 Processing sheet with id= AI, first strand: chain 'H' and resid 19 through 22 removed outlier: 6.673A pdb=" N VAL H 70 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL H 47 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU H 72 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'J' and resid 141 through 144 removed outlier: 3.523A pdb=" N GLU J 141 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA J 123 " --> pdb=" O GLN J 143 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL J 155 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU J 121 " --> pdb=" O ARG J 153 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG J 153 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'L' and resid 141 through 144 removed outlier: 3.755A pdb=" N ALA L 120 " --> pdb=" O VAL L 155 " (cutoff:3.500A) 1241 hydrogen bonds defined for protein. 3465 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: 12.83 Time building geometry restraints manager: 13.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9965 1.34 - 1.46: 4291 1.46 - 1.57: 15651 1.57 - 1.69: 9 1.69 - 1.81: 194 Bond restraints: 30110 Sorted by residual: bond pdb=" CA GLU D 296 " pdb=" C GLU D 296 " ideal model delta sigma weight residual 1.522 1.475 0.046 1.72e-02 3.38e+03 7.31e+00 bond pdb=" C MET D 445 " pdb=" N LEU D 446 " ideal model delta sigma weight residual 1.331 1.262 0.069 2.83e-02 1.25e+03 5.96e+00 bond pdb=" N MET H 1 " pdb=" CA MET H 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 ... (remaining 30105 not shown) Histogram of bond angle deviations from ideal: 99.41 - 107.49: 1258 107.49 - 115.58: 18252 115.58 - 123.66: 20535 123.66 - 131.74: 718 131.74 - 139.83: 44 Bond angle restraints: 40807 Sorted by residual: angle pdb=" N ILE A 40 " pdb=" CA ILE A 40 " pdb=" C ILE A 40 " ideal model delta sigma weight residual 113.20 110.29 2.91 9.60e-01 1.09e+00 9.19e+00 angle pdb=" C3' ATP B 601 " pdb=" C4' ATP B 601 " pdb=" C5' ATP B 601 " ideal model delta sigma weight residual 115.19 110.11 5.08 1.76e+00 3.23e-01 8.32e+00 angle pdb=" N PRO A 420 " pdb=" CA PRO A 420 " pdb=" C PRO A 420 " ideal model delta sigma weight residual 112.10 119.23 -7.13 2.60e+00 1.48e-01 7.53e+00 angle pdb=" C3' ATP C 601 " pdb=" C4' ATP C 601 " pdb=" O4' ATP C 601 " ideal model delta sigma weight residual 105.22 101.88 3.34 1.30e+00 5.94e-01 6.62e+00 angle pdb=" C PHE B 141 " pdb=" CA PHE B 141 " pdb=" CB PHE B 141 " ideal model delta sigma weight residual 110.42 115.52 -5.10 1.99e+00 2.53e-01 6.57e+00 ... (remaining 40802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.32: 18054 31.32 - 62.64: 296 62.64 - 93.96: 32 93.96 - 125.28: 0 125.28 - 156.60: 1 Dihedral angle restraints: 18383 sinusoidal: 7561 harmonic: 10822 Sorted by residual: dihedral pdb=" C5' ADP A 601 " pdb=" O5' ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 96.60 -156.60 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" CA LEU A 181 " pdb=" C LEU A 181 " pdb=" N LYS A 182 " pdb=" CA LYS A 182 " ideal model delta harmonic sigma weight residual -180.00 -155.70 -24.30 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ARG E 372 " pdb=" C ARG E 372 " pdb=" N GLU E 373 " pdb=" CA GLU E 373 " ideal model delta harmonic sigma weight residual -180.00 -157.60 -22.40 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 18380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3777 0.057 - 0.114: 721 0.114 - 0.171: 67 0.171 - 0.228: 1 0.228 - 0.285: 6 Chirality restraints: 4572 Sorted by residual: chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C2' ATP B 601 " pdb=" C1' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" O2' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C3' ATP C 601 " pdb=" C2' ATP C 601 " pdb=" C4' ATP C 601 " pdb=" O3' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 4569 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 200 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO A 201 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 201 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 201 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 446 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO F 447 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO F 447 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 447 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 542 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO A 543 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " -0.027 5.00e-02 4.00e+02 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 68 2.39 - 3.01: 18369 3.01 - 3.64: 43534 3.64 - 4.27: 69011 4.27 - 4.90: 116336 Nonbonded interactions: 247318 Sorted by model distance: nonbonded pdb=" OG SER A 235 " pdb="MG MG A 602 " model vdw 1.758 2.170 nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 1.782 2.170 nonbonded pdb=" O1B ATP C 601 " pdb="MG MG C 602 " model vdw 1.928 2.170 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 1.955 2.440 nonbonded pdb=" O LYS D 370 " pdb=" OG1 THR D 371 " model vdw 1.980 2.440 ... (remaining 247313 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 578) selection = (chain 'B' and resid 1 through 578) selection = (chain 'C' and resid 1 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 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: 6.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.250 Check model and map are aligned: 0.430 Set scattering table: 0.280 Process input model: 83.070 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:12.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 30110 Z= 0.399 Angle : 0.557 7.133 40807 Z= 0.292 Chirality : 0.045 0.285 4572 Planarity : 0.005 0.054 5333 Dihedral : 11.837 156.600 11465 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.03 % Favored : 96.94 % Rotamer: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.57 % 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: 0.65 (0.14), residues: 3764 helix: 1.51 (0.13), residues: 1546 sheet: -0.75 (0.21), residues: 611 loop : -0.02 (0.17), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 175 HIS 0.005 0.001 HIS B 145 PHE 0.016 0.002 PHE A 230 TYR 0.016 0.002 TYR B 428 ARG 0.009 0.001 ARG D 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 818 time to evaluate : 3.376 Fit side-chains revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7491 (ttp80) cc_final: 0.7128 (ttt-90) REVERT: A 107 VAL cc_start: 0.8510 (t) cc_final: 0.8306 (t) REVERT: A 130 ARG cc_start: 0.7479 (mtm110) cc_final: 0.6953 (ptt-90) REVERT: A 169 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6888 (mt-10) REVERT: A 170 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6643 (mt-10) REVERT: A 179 THR cc_start: 0.8159 (t) cc_final: 0.7491 (p) REVERT: A 343 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7558 (mt-10) REVERT: A 481 ARG cc_start: 0.7367 (mtp85) cc_final: 0.7083 (ttt90) REVERT: A 517 LYS cc_start: 0.7253 (tptp) cc_final: 0.6732 (tttt) REVERT: A 532 ARG cc_start: 0.6815 (ptt90) cc_final: 0.6546 (tmm-80) REVERT: B 3 GLN cc_start: 0.7791 (tt0) cc_final: 0.7247 (mt0) REVERT: B 124 LYS cc_start: 0.7318 (pttm) cc_final: 0.6737 (mptt) REVERT: B 209 MET cc_start: 0.7470 (mtp) cc_final: 0.7244 (mtt) REVERT: B 230 PHE cc_start: 0.5674 (p90) cc_final: 0.5148 (p90) REVERT: B 268 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6840 (tp30) REVERT: B 406 PHE cc_start: 0.7776 (t80) cc_final: 0.7287 (t80) REVERT: B 408 ARG cc_start: 0.7309 (mtp180) cc_final: 0.6971 (ttm-80) REVERT: B 509 MET cc_start: 0.6576 (mmm) cc_final: 0.5522 (tmt) REVERT: B 550 ARG cc_start: 0.5560 (mmm160) cc_final: 0.5266 (mmt90) REVERT: C 19 MET cc_start: 0.8986 (mmm) cc_final: 0.8636 (mmm) REVERT: C 93 ARG cc_start: 0.7835 (mmp80) cc_final: 0.7153 (mmm160) REVERT: C 197 ARG cc_start: 0.7419 (ttp80) cc_final: 0.7032 (ptm-80) REVERT: C 336 GLU cc_start: 0.7707 (tp30) cc_final: 0.7427 (mm-30) REVERT: C 347 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7493 (mt-10) REVERT: C 480 GLU cc_start: 0.7426 (mp0) cc_final: 0.7071 (mt-10) REVERT: C 547 ARG cc_start: 0.7364 (ttm110) cc_final: 0.7121 (ttt90) REVERT: C 567 MET cc_start: 0.7209 (mmm) cc_final: 0.6822 (mmm) REVERT: D 9 THR cc_start: 0.8569 (m) cc_final: 0.8358 (p) REVERT: D 49 GLU cc_start: 0.7939 (tt0) cc_final: 0.7532 (OUTLIER) REVERT: D 206 GLN cc_start: 0.7214 (mm-40) cc_final: 0.6710 (pt0) REVERT: D 388 ASN cc_start: 0.7466 (m-40) cc_final: 0.7245 (m-40) REVERT: D 437 GLN cc_start: 0.8151 (tt0) cc_final: 0.7851 (tt0) REVERT: E 15 SER cc_start: 0.8386 (t) cc_final: 0.7876 (p) REVERT: E 77 GLU cc_start: 0.8304 (pt0) cc_final: 0.7986 (pt0) REVERT: E 81 ARG cc_start: 0.7667 (mtm-85) cc_final: 0.7313 (mpt-90) REVERT: E 209 GLU cc_start: 0.7653 (tt0) cc_final: 0.7193 (tp30) REVERT: E 230 GLU cc_start: 0.7948 (tt0) cc_final: 0.7661 (tt0) REVERT: E 345 ARG cc_start: 0.7496 (ttm-80) cc_final: 0.6913 (mtm-85) REVERT: E 362 MET cc_start: 0.8745 (ttp) cc_final: 0.8146 (ttp) REVERT: E 461 LYS cc_start: 0.6741 (mtpt) cc_final: 0.6237 (tttt) REVERT: F 6 LYS cc_start: 0.7288 (ttpp) cc_final: 0.6903 (ptpt) REVERT: F 46 GLN cc_start: 0.9070 (tt0) cc_final: 0.8829 (tt0) REVERT: F 162 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7532 (mp0) REVERT: F 250 ASP cc_start: 0.8251 (m-30) cc_final: 0.8022 (m-30) REVERT: F 305 LYS cc_start: 0.7908 (mttt) cc_final: 0.7077 (mmmt) REVERT: F 373 GLU cc_start: 0.7121 (mp0) cc_final: 0.6835 (pm20) REVERT: G 148 LYS cc_start: 0.6223 (ttmm) cc_final: 0.5782 (tttt) REVERT: I 104 MET cc_start: 0.4639 (mtm) cc_final: 0.4228 (tmm) REVERT: J 67 LEU cc_start: 0.5734 (mt) cc_final: 0.5464 (tp) REVERT: J 113 GLU cc_start: 0.5213 (mt-10) cc_final: 0.4687 (tp30) REVERT: J 164 GLU cc_start: 0.5723 (tp30) cc_final: 0.5490 (tt0) REVERT: L 112 LEU cc_start: 0.6439 (mt) cc_final: 0.6058 (tm) outliers start: 2 outliers final: 2 residues processed: 818 average time/residue: 1.7555 time to fit residues: 1629.5809 Evaluate side-chains 449 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 448 time to evaluate : 3.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 152 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 96 optimal weight: 0.2980 chunk 190 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 292 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 217 optimal weight: 10.0000 chunk 338 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 469 GLN B 7 GLN B 145 HIS ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN B 418 HIS C 109 HIS C 501 HIS D 46 GLN D 161 ASN D 407 ASN E 23 ASN E 206 GLN E 363 ASN E 364 ASN E 448 GLN F 23 ASN F 161 ASN F 364 ASN F 388 ASN F 407 ASN F 424 ASN F 428 GLN G 22 GLN G 55 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30110 Z= 0.245 Angle : 0.576 12.382 40807 Z= 0.295 Chirality : 0.045 0.201 4572 Planarity : 0.005 0.062 5333 Dihedral : 6.553 139.752 4261 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.21 % Favored : 97.77 % Rotamer: Outliers : 4.12 % Allowed : 12.62 % Favored : 83.26 % 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: 0.79 (0.14), residues: 3764 helix: 1.49 (0.13), residues: 1564 sheet: -0.47 (0.21), residues: 617 loop : 0.10 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 175 HIS 0.004 0.001 HIS F 249 PHE 0.012 0.002 PHE C 574 TYR 0.016 0.002 TYR B 428 ARG 0.007 0.001 ARG C 488 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 459 time to evaluate : 3.711 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7737 (mt0) REVERT: A 54 ASP cc_start: 0.7698 (t70) cc_final: 0.7052 (t70) REVERT: A 95 ARG cc_start: 0.7547 (ttp80) cc_final: 0.7310 (ttt-90) REVERT: A 104 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.6358 (mtp85) REVERT: A 124 LYS cc_start: 0.7698 (mmmt) cc_final: 0.7037 (mppt) REVERT: A 130 ARG cc_start: 0.7599 (mtm110) cc_final: 0.6926 (ptt-90) REVERT: A 158 LYS cc_start: 0.7334 (tttt) cc_final: 0.7058 (ttmm) REVERT: A 170 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6642 (mt-10) REVERT: A 343 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7537 (mt-10) REVERT: A 481 ARG cc_start: 0.7446 (mtp85) cc_final: 0.6940 (ttm110) REVERT: A 517 LYS cc_start: 0.7305 (tptp) cc_final: 0.6797 (tttt) REVERT: A 524 LYS cc_start: 0.7858 (ttpp) cc_final: 0.7361 (tttt) REVERT: A 532 ARG cc_start: 0.6487 (ptt90) cc_final: 0.6068 (ptt-90) REVERT: B 3 GLN cc_start: 0.7793 (tt0) cc_final: 0.7181 (mt0) REVERT: B 38 GLU cc_start: 0.7334 (pt0) cc_final: 0.7111 (tt0) REVERT: B 69 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7908 (mt) REVERT: B 124 LYS cc_start: 0.7489 (pttm) cc_final: 0.6888 (mptt) REVERT: B 246 ASN cc_start: 0.6965 (t0) cc_final: 0.6718 (t0) REVERT: B 401 ARG cc_start: 0.7027 (mtp85) cc_final: 0.6638 (mtt-85) REVERT: B 406 PHE cc_start: 0.7638 (t80) cc_final: 0.7430 (t80) REVERT: B 408 ARG cc_start: 0.7352 (mtp180) cc_final: 0.7040 (ttm-80) REVERT: B 454 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8169 (mp) REVERT: B 509 MET cc_start: 0.6595 (mmm) cc_final: 0.5627 (tmt) REVERT: C 85 ASP cc_start: 0.6865 (t0) cc_final: 0.6557 (t0) REVERT: C 96 GLU cc_start: 0.7532 (pp20) cc_final: 0.7305 (pt0) REVERT: C 182 LYS cc_start: 0.8151 (mttt) cc_final: 0.7671 (mtmm) REVERT: C 197 ARG cc_start: 0.7513 (ttp80) cc_final: 0.7124 (ptm-80) REVERT: C 300 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7209 (tm-30) REVERT: C 336 GLU cc_start: 0.7829 (tp30) cc_final: 0.7596 (tp30) REVERT: C 347 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7536 (mt-10) REVERT: C 517 LYS cc_start: 0.7966 (tttt) cc_final: 0.7720 (tttm) REVERT: C 547 ARG cc_start: 0.7425 (ttm110) cc_final: 0.6887 (ttt90) REVERT: C 567 MET cc_start: 0.7214 (mmm) cc_final: 0.6755 (mmm) REVERT: D 9 THR cc_start: 0.8590 (m) cc_final: 0.8351 (p) REVERT: D 49 GLU cc_start: 0.8046 (tt0) cc_final: 0.7650 (tm-30) REVERT: D 206 GLN cc_start: 0.7342 (mm-40) cc_final: 0.6897 (pt0) REVERT: D 274 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.6886 (mtp180) REVERT: D 388 ASN cc_start: 0.7504 (m-40) cc_final: 0.7250 (m-40) REVERT: D 401 GLU cc_start: 0.5948 (mp0) cc_final: 0.5484 (pm20) REVERT: E 77 GLU cc_start: 0.8233 (pt0) cc_final: 0.7892 (pt0) REVERT: E 81 ARG cc_start: 0.7544 (mtm-85) cc_final: 0.7191 (mpt-90) REVERT: E 162 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: E 209 GLU cc_start: 0.7647 (tt0) cc_final: 0.7222 (tp30) REVERT: E 248 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7250 (tt0) REVERT: E 336 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7581 (pm20) REVERT: E 338 GLN cc_start: 0.8520 (tt0) cc_final: 0.8288 (tp40) REVERT: E 345 ARG cc_start: 0.7527 (ttm-80) cc_final: 0.6936 (mtm-85) REVERT: E 416 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.6938 (t70) REVERT: F 6 LYS cc_start: 0.7273 (ttpp) cc_final: 0.6856 (ptpt) REVERT: F 46 GLN cc_start: 0.9079 (tt0) cc_final: 0.8838 (tt0) REVERT: F 162 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7566 (mp0) REVERT: F 250 ASP cc_start: 0.8266 (m-30) cc_final: 0.8054 (m-30) REVERT: F 305 LYS cc_start: 0.7932 (mttt) cc_final: 0.7071 (mmmt) REVERT: F 453 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8151 (mtt180) REVERT: G 13 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8151 (tm-30) REVERT: G 159 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6711 (mtt90) REVERT: G 181 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7632 (mp10) REVERT: I 104 MET cc_start: 0.4608 (mtm) cc_final: 0.4310 (tmm) REVERT: J 66 LEU cc_start: 0.5195 (mp) cc_final: 0.4889 (pt) REVERT: J 113 GLU cc_start: 0.5292 (mt-10) cc_final: 0.4606 (tp30) REVERT: J 164 GLU cc_start: 0.5868 (tp30) cc_final: 0.5418 (tt0) REVERT: K 104 MET cc_start: 0.5646 (OUTLIER) cc_final: 0.4415 (mpp) REVERT: L 102 GLU cc_start: 0.5233 (mm-30) cc_final: 0.4906 (tm-30) REVERT: L 167 LEU cc_start: 0.6538 (mm) cc_final: 0.6263 (mm) outliers start: 127 outliers final: 39 residues processed: 536 average time/residue: 1.6509 time to fit residues: 1016.8513 Evaluate side-chains 446 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 394 time to evaluate : 3.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 453 ARG Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 138 ARG Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 281 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 339 optimal weight: 8.9990 chunk 366 optimal weight: 2.9990 chunk 302 optimal weight: 5.9990 chunk 336 optimal weight: 0.0570 chunk 115 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 overall best weight: 2.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 GLN B 7 GLN B 397 GLN C 3 GLN C 109 HIS ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 GLN D 407 ASN E 23 ASN E 249 HIS E 310 GLN E 363 ASN E 448 GLN F 23 ASN F 166 GLN F 363 ASN G 22 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 30110 Z= 0.404 Angle : 0.658 9.142 40807 Z= 0.335 Chirality : 0.048 0.250 4572 Planarity : 0.006 0.055 5333 Dihedral : 6.771 121.795 4259 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.60 % Favored : 97.37 % Rotamer: Outliers : 4.87 % Allowed : 14.69 % Favored : 80.44 % 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: 0.37 (0.14), residues: 3764 helix: 1.02 (0.13), residues: 1568 sheet: -0.39 (0.21), residues: 587 loop : -0.15 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 100 HIS 0.007 0.002 HIS D 252 PHE 0.018 0.002 PHE C 230 TYR 0.020 0.002 TYR F 203 ARG 0.006 0.001 ARG L 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 401 time to evaluate : 3.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: A 54 ASP cc_start: 0.7837 (t70) cc_final: 0.7231 (t70) REVERT: A 93 ARG cc_start: 0.7716 (mmp80) cc_final: 0.7442 (mmp80) REVERT: A 95 ARG cc_start: 0.7656 (ttp80) cc_final: 0.7430 (ttt-90) REVERT: A 98 THR cc_start: 0.7668 (OUTLIER) cc_final: 0.7220 (p) REVERT: A 104 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.6444 (mtp85) REVERT: A 124 LYS cc_start: 0.7724 (mmmt) cc_final: 0.7045 (mppt) REVERT: A 130 ARG cc_start: 0.7610 (mtm110) cc_final: 0.6839 (ptt-90) REVERT: A 176 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6530 (pt0) REVERT: A 456 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: A 481 ARG cc_start: 0.7553 (mtp85) cc_final: 0.7003 (ttm110) REVERT: A 488 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7529 (ttp80) REVERT: A 517 LYS cc_start: 0.7246 (tptp) cc_final: 0.6833 (tttt) REVERT: A 532 ARG cc_start: 0.6683 (ptt90) cc_final: 0.6195 (ptt-90) REVERT: B 69 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7820 (mt) REVERT: B 122 MET cc_start: 0.6954 (mtt) cc_final: 0.6592 (mtp) REVERT: B 133 MET cc_start: 0.7995 (mtm) cc_final: 0.7654 (mtp) REVERT: B 246 ASN cc_start: 0.7141 (t0) cc_final: 0.6845 (t0) REVERT: B 268 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6650 (mm-30) REVERT: B 397 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7439 (tt0) REVERT: B 401 ARG cc_start: 0.7277 (mtp85) cc_final: 0.6724 (mtt-85) REVERT: B 406 PHE cc_start: 0.7791 (t80) cc_final: 0.7480 (t80) REVERT: B 408 ARG cc_start: 0.7287 (mtp180) cc_final: 0.7083 (ttm-80) REVERT: B 454 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8164 (mp) REVERT: B 509 MET cc_start: 0.6619 (mmm) cc_final: 0.5826 (tmm) REVERT: B 520 LEU cc_start: 0.6530 (tt) cc_final: 0.6192 (mp) REVERT: C 96 GLU cc_start: 0.7539 (pp20) cc_final: 0.7283 (pt0) REVERT: C 137 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8372 (m) REVERT: C 197 ARG cc_start: 0.7581 (ttp80) cc_final: 0.7103 (ptm-80) REVERT: C 300 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: C 336 GLU cc_start: 0.7984 (tp30) cc_final: 0.7510 (mm-30) REVERT: C 347 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7540 (mt-10) REVERT: C 375 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7552 (tm-30) REVERT: C 517 LYS cc_start: 0.8042 (tttt) cc_final: 0.7800 (tttp) REVERT: C 546 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6504 (tt0) REVERT: C 547 ARG cc_start: 0.7671 (ttm110) cc_final: 0.7053 (ttt90) REVERT: C 550 ARG cc_start: 0.7666 (mmm160) cc_final: 0.6932 (mtt180) REVERT: C 567 MET cc_start: 0.7259 (mmm) cc_final: 0.6669 (mmm) REVERT: D 9 THR cc_start: 0.8438 (m) cc_final: 0.8212 (p) REVERT: D 126 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7683 (ttpp) REVERT: D 206 GLN cc_start: 0.7334 (mm-40) cc_final: 0.6861 (pt0) REVERT: D 305 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7675 (mtpm) REVERT: D 388 ASN cc_start: 0.7391 (m-40) cc_final: 0.7161 (m-40) REVERT: D 407 ASN cc_start: 0.6514 (OUTLIER) cc_final: 0.6188 (m110) REVERT: E 81 ARG cc_start: 0.7577 (mtm-85) cc_final: 0.7320 (mpt-90) REVERT: E 109 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6716 (tp30) REVERT: E 209 GLU cc_start: 0.7707 (tt0) cc_final: 0.7268 (tp30) REVERT: E 336 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7542 (pm20) REVERT: E 338 GLN cc_start: 0.8574 (tt0) cc_final: 0.8242 (tp40) REVERT: E 345 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.6876 (mtm-85) REVERT: E 416 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.6996 (t70) REVERT: F 6 LYS cc_start: 0.7411 (ttpp) cc_final: 0.6962 (ptpt) REVERT: F 46 GLN cc_start: 0.9134 (tt0) cc_final: 0.8882 (tt0) REVERT: F 88 MET cc_start: 0.9001 (mtm) cc_final: 0.8747 (mtt) REVERT: F 162 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7688 (mm-30) REVERT: F 305 LYS cc_start: 0.7924 (mttt) cc_final: 0.7081 (ptmm) REVERT: F 388 ASN cc_start: 0.7863 (OUTLIER) cc_final: 0.7354 (m110) REVERT: G 13 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: G 159 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6734 (mtt90) REVERT: G 181 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7850 (mp10) REVERT: G 196 ARG cc_start: 0.7808 (mtp-110) cc_final: 0.7589 (mtp-110) REVERT: I 104 MET cc_start: 0.4688 (mtm) cc_final: 0.4049 (tmm) REVERT: J 67 LEU cc_start: 0.5671 (mt) cc_final: 0.5013 (tp) REVERT: J 113 GLU cc_start: 0.5125 (mt-10) cc_final: 0.4518 (tp30) REVERT: J 164 GLU cc_start: 0.6231 (tp30) cc_final: 0.5385 (tt0) REVERT: K 104 MET cc_start: 0.5889 (OUTLIER) cc_final: 0.4740 (mpp) REVERT: L 67 LEU cc_start: 0.5058 (OUTLIER) cc_final: 0.4704 (mm) REVERT: L 102 GLU cc_start: 0.5025 (tm-30) cc_final: 0.4806 (tm-30) REVERT: L 112 LEU cc_start: 0.5993 (OUTLIER) cc_final: 0.5679 (mm) outliers start: 150 outliers final: 66 residues processed: 501 average time/residue: 1.6053 time to fit residues: 925.5183 Evaluate side-chains 456 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 364 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 397 GLN Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 510 LYS Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 126 LYS Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 384 SER Chi-restraints excluded: chain D residue 407 ASN Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 452 LYS Chi-restraints excluded: chain F residue 453 ARG Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 138 ARG Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 155 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 chunk 227 optimal weight: 0.5980 chunk 340 optimal weight: 0.0270 chunk 360 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 322 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 overall best weight: 1.7244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 GLN C 3 GLN C 109 HIS ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 ASN E 23 ASN E 363 ASN G 22 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 30110 Z= 0.304 Angle : 0.592 8.871 40807 Z= 0.300 Chirality : 0.045 0.247 4572 Planarity : 0.005 0.052 5333 Dihedral : 6.556 115.176 4259 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.34 % Favored : 97.64 % Rotamer: Outliers : 5.22 % Allowed : 15.86 % Favored : 78.92 % 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: 0.38 (0.14), residues: 3764 helix: 1.02 (0.13), residues: 1569 sheet: -0.37 (0.22), residues: 575 loop : -0.14 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 119 HIS 0.004 0.001 HIS F 344 PHE 0.014 0.002 PHE E 130 TYR 0.019 0.002 TYR A 439 ARG 0.006 0.001 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 374 time to evaluate : 3.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: A 92 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6316 (mp0) REVERT: A 98 THR cc_start: 0.7608 (m) cc_final: 0.7247 (p) REVERT: A 104 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.6460 (mtp85) REVERT: A 124 LYS cc_start: 0.7716 (mmmt) cc_final: 0.7041 (mppt) REVERT: A 130 ARG cc_start: 0.7647 (mtm110) cc_final: 0.6824 (ptt-90) REVERT: A 176 GLU cc_start: 0.6833 (mm-30) cc_final: 0.6544 (pt0) REVERT: A 410 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7915 (m-30) REVERT: A 456 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: A 481 ARG cc_start: 0.7544 (mtp85) cc_final: 0.7026 (ttm110) REVERT: A 488 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7553 (ttp80) REVERT: A 517 LYS cc_start: 0.7221 (tptp) cc_final: 0.6816 (tttt) REVERT: A 524 LYS cc_start: 0.7792 (ttpp) cc_final: 0.7315 (tttt) REVERT: A 532 ARG cc_start: 0.6559 (ptt90) cc_final: 0.6012 (ptt-90) REVERT: B 69 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7820 (mt) REVERT: B 122 MET cc_start: 0.7048 (mtt) cc_final: 0.6709 (mtp) REVERT: B 133 MET cc_start: 0.7947 (mtm) cc_final: 0.7589 (mtp) REVERT: B 246 ASN cc_start: 0.7053 (t0) cc_final: 0.6661 (t0) REVERT: B 268 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6654 (mm-30) REVERT: B 401 ARG cc_start: 0.7248 (mtp85) cc_final: 0.6739 (mtt-85) REVERT: B 406 PHE cc_start: 0.7758 (t80) cc_final: 0.7448 (t80) REVERT: B 408 ARG cc_start: 0.7195 (mtp180) cc_final: 0.6955 (ttm-80) REVERT: B 509 MET cc_start: 0.6589 (mmm) cc_final: 0.5828 (tmm) REVERT: B 520 LEU cc_start: 0.6466 (tt) cc_final: 0.6192 (mt) REVERT: B 550 ARG cc_start: 0.6659 (tpt170) cc_final: 0.6413 (tpm170) REVERT: C 96 GLU cc_start: 0.7558 (pp20) cc_final: 0.7314 (pt0) REVERT: C 137 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8366 (m) REVERT: C 197 ARG cc_start: 0.7544 (ttp80) cc_final: 0.7093 (ptm-80) REVERT: C 220 MET cc_start: 0.7875 (tpt) cc_final: 0.7568 (tpt) REVERT: C 276 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.6738 (ptpt) REVERT: C 300 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7370 (tm-30) REVERT: C 336 GLU cc_start: 0.7975 (tp30) cc_final: 0.7458 (mm-30) REVERT: C 375 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: C 517 LYS cc_start: 0.8019 (tttt) cc_final: 0.7800 (tttp) REVERT: C 546 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6663 (tt0) REVERT: C 547 ARG cc_start: 0.7550 (ttm110) cc_final: 0.6994 (ttt90) REVERT: C 567 MET cc_start: 0.7249 (mmm) cc_final: 0.6698 (mmm) REVERT: D 49 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8172 (tt0) REVERT: D 126 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7685 (ttpp) REVERT: D 206 GLN cc_start: 0.7319 (mm-40) cc_final: 0.6820 (pt0) REVERT: D 388 ASN cc_start: 0.7386 (m-40) cc_final: 0.7170 (m-40) REVERT: D 466 LYS cc_start: 0.7401 (mmmt) cc_final: 0.6096 (mppt) REVERT: E 77 GLU cc_start: 0.8259 (pt0) cc_final: 0.7965 (pt0) REVERT: E 81 ARG cc_start: 0.7615 (mtm-85) cc_final: 0.7219 (mpt-90) REVERT: E 109 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6667 (tp30) REVERT: E 209 GLU cc_start: 0.7779 (tt0) cc_final: 0.7338 (tp30) REVERT: E 336 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.7545 (pm20) REVERT: E 345 ARG cc_start: 0.7458 (ttm-80) cc_final: 0.6937 (mtm-85) REVERT: E 416 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7074 (t70) REVERT: E 420 ARG cc_start: 0.7159 (ttp-110) cc_final: 0.6886 (ttp-110) REVERT: F 6 LYS cc_start: 0.7344 (ttpp) cc_final: 0.6957 (ptpt) REVERT: F 46 GLN cc_start: 0.9124 (tt0) cc_final: 0.8922 (tt0) REVERT: F 88 MET cc_start: 0.9007 (mtm) cc_final: 0.8787 (mtt) REVERT: F 162 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7669 (mp0) REVERT: F 305 LYS cc_start: 0.7962 (mttt) cc_final: 0.7207 (mmmt) REVERT: F 388 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7294 (m110) REVERT: G 13 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8170 (tm-30) REVERT: G 159 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6819 (mtt90) REVERT: G 200 LYS cc_start: 0.7168 (mmmt) cc_final: 0.6623 (mtpt) REVERT: H 63 MET cc_start: 0.3528 (pmm) cc_final: 0.3325 (pmm) REVERT: I 104 MET cc_start: 0.4731 (mtm) cc_final: 0.4011 (tmm) REVERT: J 66 LEU cc_start: 0.4982 (mp) cc_final: 0.4707 (pt) REVERT: J 113 GLU cc_start: 0.5301 (mt-10) cc_final: 0.4490 (tp30) REVERT: J 149 ARG cc_start: 0.1938 (tpt90) cc_final: 0.1669 (pmm150) REVERT: K 104 MET cc_start: 0.5673 (OUTLIER) cc_final: 0.4432 (mpp) REVERT: L 67 LEU cc_start: 0.5182 (OUTLIER) cc_final: 0.4807 (mm) REVERT: L 102 GLU cc_start: 0.5083 (tm-30) cc_final: 0.4877 (tm-30) REVERT: L 130 HIS cc_start: 0.4861 (OUTLIER) cc_final: 0.4389 (m90) REVERT: L 150 LEU cc_start: 0.6527 (mt) cc_final: 0.6312 (mm) outliers start: 161 outliers final: 72 residues processed: 487 average time/residue: 1.6205 time to fit residues: 908.4824 Evaluate side-chains 452 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 356 time to evaluate : 3.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 126 LYS Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 130 HIS Chi-restraints excluded: chain L residue 138 ARG Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 148 optimal weight: 0.3980 chunk 307 optimal weight: 0.6980 chunk 249 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 184 optimal weight: 0.6980 chunk 323 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN C 109 HIS E 23 ASN F 23 ASN F 142 ASN F 388 ASN G 22 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30110 Z= 0.177 Angle : 0.520 8.245 40807 Z= 0.261 Chirality : 0.042 0.152 4572 Planarity : 0.005 0.046 5333 Dihedral : 6.182 109.417 4259 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.02 % Favored : 97.95 % Rotamer: Outliers : 4.31 % Allowed : 17.32 % Favored : 78.37 % 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: 0.69 (0.14), residues: 3764 helix: 1.31 (0.13), residues: 1577 sheet: -0.32 (0.21), residues: 586 loop : 0.04 (0.16), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 119 HIS 0.003 0.001 HIS C 418 PHE 0.012 0.001 PHE E 130 TYR 0.017 0.001 TYR A 439 ARG 0.009 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 384 time to evaluate : 3.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7748 (t70) cc_final: 0.7224 (t70) REVERT: A 92 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6306 (mp0) REVERT: A 98 THR cc_start: 0.7601 (OUTLIER) cc_final: 0.7258 (p) REVERT: A 104 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.6396 (mtp85) REVERT: A 124 LYS cc_start: 0.7726 (mmmt) cc_final: 0.7048 (mppt) REVERT: A 130 ARG cc_start: 0.7658 (mtm110) cc_final: 0.6788 (ptt-90) REVERT: A 176 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6605 (pt0) REVERT: A 456 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7242 (tm-30) REVERT: A 481 ARG cc_start: 0.7536 (mtp85) cc_final: 0.7021 (ttm110) REVERT: A 517 LYS cc_start: 0.7116 (tptp) cc_final: 0.6745 (tttt) REVERT: A 524 LYS cc_start: 0.7754 (ttpp) cc_final: 0.7287 (tttt) REVERT: B 69 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7907 (mt) REVERT: B 122 MET cc_start: 0.7063 (mtt) cc_final: 0.6729 (mtp) REVERT: B 133 MET cc_start: 0.7933 (mtm) cc_final: 0.7557 (mtp) REVERT: B 246 ASN cc_start: 0.6985 (t0) cc_final: 0.6643 (t0) REVERT: B 401 ARG cc_start: 0.7252 (mtp85) cc_final: 0.6789 (mtt-85) REVERT: B 406 PHE cc_start: 0.7663 (t80) cc_final: 0.7405 (t80) REVERT: B 408 ARG cc_start: 0.7162 (mtp180) cc_final: 0.6915 (ttm-80) REVERT: B 509 MET cc_start: 0.6508 (mmm) cc_final: 0.5800 (tmt) REVERT: B 545 LEU cc_start: 0.5505 (mm) cc_final: 0.5213 (tp) REVERT: C 45 ASP cc_start: 0.8424 (t70) cc_final: 0.8166 (t70) REVERT: C 96 GLU cc_start: 0.7525 (pp20) cc_final: 0.7318 (pt0) REVERT: C 137 THR cc_start: 0.8686 (t) cc_final: 0.8264 (m) REVERT: C 197 ARG cc_start: 0.7541 (ttp80) cc_final: 0.7118 (ptm-80) REVERT: C 276 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.6676 (ptpt) REVERT: C 300 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: C 336 GLU cc_start: 0.7923 (tp30) cc_final: 0.7412 (mm-30) REVERT: C 517 LYS cc_start: 0.8035 (tttt) cc_final: 0.7810 (tttm) REVERT: C 540 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6835 (tt) REVERT: C 546 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6494 (tt0) REVERT: C 547 ARG cc_start: 0.7518 (ttm110) cc_final: 0.6991 (ttt90) REVERT: C 567 MET cc_start: 0.7266 (mmm) cc_final: 0.6713 (mmm) REVERT: D 49 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: D 62 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.6027 (mm-30) REVERT: D 206 GLN cc_start: 0.7271 (mm-40) cc_final: 0.6803 (pt0) REVERT: D 248 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7158 (mm-30) REVERT: D 388 ASN cc_start: 0.7352 (m-40) cc_final: 0.7139 (m-40) REVERT: D 466 LYS cc_start: 0.7368 (mmmt) cc_final: 0.6084 (mppt) REVERT: E 77 GLU cc_start: 0.8065 (pt0) cc_final: 0.7713 (pt0) REVERT: E 81 ARG cc_start: 0.7590 (mtm-85) cc_final: 0.7135 (mpt-90) REVERT: E 109 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6651 (tp30) REVERT: E 209 GLU cc_start: 0.7766 (tt0) cc_final: 0.7429 (mm-30) REVERT: E 336 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: E 338 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8574 (tp40) REVERT: E 345 ARG cc_start: 0.7445 (ttm-80) cc_final: 0.6913 (mtm-85) REVERT: E 416 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7085 (t70) REVERT: F 3 LEU cc_start: 0.6603 (tp) cc_final: 0.6238 (tp) REVERT: F 6 LYS cc_start: 0.7262 (ttpp) cc_final: 0.6933 (ptpt) REVERT: F 46 GLN cc_start: 0.9103 (tt0) cc_final: 0.8900 (tt0) REVERT: F 88 MET cc_start: 0.9003 (mtm) cc_final: 0.8791 (mtt) REVERT: F 162 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7651 (mp0) REVERT: F 178 SER cc_start: 0.8285 (t) cc_final: 0.7945 (p) REVERT: F 305 LYS cc_start: 0.7962 (mttt) cc_final: 0.7168 (mmmt) REVERT: F 345 ARG cc_start: 0.8220 (mmt90) cc_final: 0.7990 (mtt180) REVERT: G 13 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8155 (tm-30) REVERT: G 159 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6851 (mtt90) REVERT: H 103 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6462 (tmmm) REVERT: I 104 MET cc_start: 0.4709 (mtm) cc_final: 0.4028 (tmm) REVERT: J 66 LEU cc_start: 0.5062 (mp) cc_final: 0.4738 (pt) REVERT: J 113 GLU cc_start: 0.5038 (mt-10) cc_final: 0.4627 (tp30) REVERT: K 104 MET cc_start: 0.5558 (OUTLIER) cc_final: 0.4304 (mpp) REVERT: L 67 LEU cc_start: 0.5015 (OUTLIER) cc_final: 0.4625 (mm) REVERT: L 130 HIS cc_start: 0.4889 (OUTLIER) cc_final: 0.4353 (m90) outliers start: 133 outliers final: 57 residues processed: 479 average time/residue: 1.6061 time to fit residues: 885.6352 Evaluate side-chains 445 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 367 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 338 GLN Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 159 ARG Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 130 HIS Chi-restraints excluded: chain L residue 138 ARG Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 2.9990 chunk 324 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 211 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 360 optimal weight: 4.9990 chunk 299 optimal weight: 0.0770 chunk 167 optimal weight: 0.1980 chunk 30 optimal weight: 0.1980 chunk 119 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN C 109 HIS ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 ASN E 427 GLN F 448 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30110 Z= 0.195 Angle : 0.528 10.497 40807 Z= 0.264 Chirality : 0.043 0.174 4572 Planarity : 0.005 0.047 5333 Dihedral : 6.075 104.085 4259 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.21 % Favored : 97.77 % Rotamer: Outliers : 4.70 % Allowed : 17.84 % Favored : 77.46 % 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: 0.78 (0.14), residues: 3764 helix: 1.36 (0.13), residues: 1581 sheet: -0.28 (0.21), residues: 599 loop : 0.13 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 100 HIS 0.003 0.001 HIS B 145 PHE 0.012 0.001 PHE E 130 TYR 0.018 0.001 TYR A 439 ARG 0.011 0.000 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 375 time to evaluate : 3.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6325 (mp0) REVERT: A 98 THR cc_start: 0.7634 (OUTLIER) cc_final: 0.7285 (p) REVERT: A 104 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.6380 (mtp85) REVERT: A 115 LYS cc_start: 0.8077 (ttmp) cc_final: 0.7806 (tttp) REVERT: A 124 LYS cc_start: 0.7689 (mmmt) cc_final: 0.7016 (mppt) REVERT: A 130 ARG cc_start: 0.7671 (mtm110) cc_final: 0.6728 (ptt-90) REVERT: A 154 ARG cc_start: 0.7173 (ptm160) cc_final: 0.6475 (ptp90) REVERT: A 170 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6236 (mt-10) REVERT: A 176 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6605 (pt0) REVERT: A 410 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7677 (m-30) REVERT: A 449 GLU cc_start: 0.8082 (mp0) cc_final: 0.7823 (mp0) REVERT: A 456 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: A 481 ARG cc_start: 0.7554 (mtp85) cc_final: 0.7008 (ttm110) REVERT: A 488 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7570 (ttp80) REVERT: A 517 LYS cc_start: 0.7104 (tptp) cc_final: 0.6733 (tttt) REVERT: A 524 LYS cc_start: 0.7803 (ttpp) cc_final: 0.7313 (tttt) REVERT: B 69 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7920 (mt) REVERT: B 122 MET cc_start: 0.7058 (mtt) cc_final: 0.6720 (mtp) REVERT: B 133 MET cc_start: 0.7929 (mtm) cc_final: 0.7569 (mtp) REVERT: B 246 ASN cc_start: 0.6960 (t0) cc_final: 0.6659 (t0) REVERT: B 401 ARG cc_start: 0.7311 (mtp85) cc_final: 0.6788 (mtt-85) REVERT: B 406 PHE cc_start: 0.7701 (t80) cc_final: 0.7428 (t80) REVERT: B 435 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7572 (mp) REVERT: B 509 MET cc_start: 0.6633 (mmm) cc_final: 0.5574 (tmm) REVERT: B 545 LEU cc_start: 0.5500 (mm) cc_final: 0.5091 (tp) REVERT: C 45 ASP cc_start: 0.8424 (t70) cc_final: 0.8180 (t70) REVERT: C 137 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8256 (m) REVERT: C 197 ARG cc_start: 0.7598 (ttp80) cc_final: 0.7132 (ptm-80) REVERT: C 276 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6650 (ptpt) REVERT: C 300 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: C 336 GLU cc_start: 0.7953 (tp30) cc_final: 0.7450 (mm-30) REVERT: C 517 LYS cc_start: 0.8026 (tttt) cc_final: 0.7810 (tttm) REVERT: C 546 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6509 (tt0) REVERT: C 547 ARG cc_start: 0.7559 (ttm110) cc_final: 0.7008 (ttt90) REVERT: C 563 PHE cc_start: 0.8245 (t80) cc_final: 0.7958 (t80) REVERT: C 567 MET cc_start: 0.7237 (mmm) cc_final: 0.6648 (mmm) REVERT: D 9 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8253 (p) REVERT: D 49 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: D 62 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5977 (mm-30) REVERT: D 206 GLN cc_start: 0.7246 (mm-40) cc_final: 0.6790 (pt0) REVERT: D 248 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7145 (mm-30) REVERT: D 466 LYS cc_start: 0.7373 (mmmt) cc_final: 0.6045 (mppt) REVERT: E 77 GLU cc_start: 0.8046 (pt0) cc_final: 0.7703 (pt0) REVERT: E 81 ARG cc_start: 0.7552 (mtm-85) cc_final: 0.7144 (mpt-90) REVERT: E 109 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6632 (tp30) REVERT: E 209 GLU cc_start: 0.7777 (tt0) cc_final: 0.7447 (mm-30) REVERT: E 336 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7483 (pm20) REVERT: E 338 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8583 (tp40) REVERT: E 345 ARG cc_start: 0.7459 (ttm-80) cc_final: 0.6774 (mtm-85) REVERT: E 416 ASP cc_start: 0.7475 (OUTLIER) cc_final: 0.7014 (t70) REVERT: F 3 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6171 (tp) REVERT: F 6 LYS cc_start: 0.7242 (ttpp) cc_final: 0.6919 (ptpt) REVERT: F 46 GLN cc_start: 0.9112 (tt0) cc_final: 0.8901 (tt0) REVERT: F 88 MET cc_start: 0.9021 (mtm) cc_final: 0.8816 (mtt) REVERT: F 162 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7644 (mp0) REVERT: F 178 SER cc_start: 0.8320 (t) cc_final: 0.7936 (p) REVERT: F 305 LYS cc_start: 0.7959 (mttt) cc_final: 0.7156 (mmmt) REVERT: F 388 ASN cc_start: 0.7747 (OUTLIER) cc_final: 0.7227 (m110) REVERT: G 200 LYS cc_start: 0.7014 (mmmt) cc_final: 0.6472 (mmtt) REVERT: H 63 MET cc_start: 0.3349 (pmm) cc_final: 0.3125 (pmm) REVERT: H 95 ARG cc_start: 0.6087 (OUTLIER) cc_final: 0.5826 (tmt170) REVERT: H 103 LYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6462 (tmmm) REVERT: I 104 MET cc_start: 0.4651 (mtm) cc_final: 0.4077 (tmm) REVERT: J 67 LEU cc_start: 0.5474 (mt) cc_final: 0.4879 (tp) REVERT: J 110 GLU cc_start: 0.5742 (OUTLIER) cc_final: 0.5501 (tp30) REVERT: K 104 MET cc_start: 0.5516 (OUTLIER) cc_final: 0.4279 (mpp) REVERT: L 67 LEU cc_start: 0.5120 (OUTLIER) cc_final: 0.4688 (mm) REVERT: L 130 HIS cc_start: 0.4936 (OUTLIER) cc_final: 0.4393 (m90) REVERT: L 150 LEU cc_start: 0.6530 (mt) cc_final: 0.6290 (mm) outliers start: 145 outliers final: 70 residues processed: 477 average time/residue: 1.6214 time to fit residues: 895.9936 Evaluate side-chains 456 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 358 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 338 GLN Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 394 LYS Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 145 GLU Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 130 HIS Chi-restraints excluded: chain L residue 138 ARG Chi-restraints excluded: chain L residue 141 GLU 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: 5.9990 chunk 205 optimal weight: 0.9990 chunk 263 optimal weight: 5.9990 chunk 204 optimal weight: 0.9980 chunk 303 optimal weight: 0.3980 chunk 201 optimal weight: 0.9980 chunk 359 optimal weight: 9.9990 chunk 224 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN C 109 HIS E 23 ASN F 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30110 Z= 0.186 Angle : 0.514 8.110 40807 Z= 0.258 Chirality : 0.043 0.169 4572 Planarity : 0.005 0.046 5333 Dihedral : 5.968 99.058 4259 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.18 % Favored : 97.79 % Rotamer: Outliers : 4.48 % Allowed : 18.33 % Favored : 77.20 % 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: 3764 helix: 1.39 (0.13), residues: 1579 sheet: -0.18 (0.21), residues: 589 loop : 0.17 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 100 HIS 0.002 0.001 HIS C 185 PHE 0.012 0.001 PHE E 130 TYR 0.020 0.001 TYR E 13 ARG 0.011 0.000 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 362 time to evaluate : 4.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6345 (mp0) REVERT: A 98 THR cc_start: 0.7629 (OUTLIER) cc_final: 0.7283 (p) REVERT: A 104 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.6307 (mtp85) REVERT: A 115 LYS cc_start: 0.8042 (ttmp) cc_final: 0.7776 (tttp) REVERT: A 124 LYS cc_start: 0.7693 (mmmt) cc_final: 0.7017 (mppt) REVERT: A 130 ARG cc_start: 0.7659 (mtm110) cc_final: 0.6738 (ptt-90) REVERT: A 154 ARG cc_start: 0.7149 (ptm160) cc_final: 0.6472 (ptp90) REVERT: A 170 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6270 (mt-10) REVERT: A 410 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7816 (m-30) REVERT: A 449 GLU cc_start: 0.8087 (mp0) cc_final: 0.7830 (mp0) REVERT: A 456 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7219 (tm-30) REVERT: A 481 ARG cc_start: 0.7515 (mtp85) cc_final: 0.6992 (ttm110) REVERT: A 517 LYS cc_start: 0.7038 (tptp) cc_final: 0.6725 (tttt) REVERT: A 524 LYS cc_start: 0.7789 (ttpp) cc_final: 0.7301 (tttt) REVERT: B 122 MET cc_start: 0.7087 (mtt) cc_final: 0.6744 (mtp) REVERT: B 133 MET cc_start: 0.7921 (mtm) cc_final: 0.7570 (mtp) REVERT: B 246 ASN cc_start: 0.6961 (t0) cc_final: 0.6740 (t0) REVERT: B 268 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6728 (tp30) REVERT: B 401 ARG cc_start: 0.7262 (mtp85) cc_final: 0.6804 (mtt-85) REVERT: B 406 PHE cc_start: 0.7682 (t80) cc_final: 0.7373 (t80) REVERT: B 520 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7136 (mp) REVERT: B 545 LEU cc_start: 0.5520 (mm) cc_final: 0.5064 (tp) REVERT: C 45 ASP cc_start: 0.8420 (t70) cc_final: 0.8153 (t70) REVERT: C 137 THR cc_start: 0.8666 (t) cc_final: 0.8268 (m) REVERT: C 197 ARG cc_start: 0.7582 (ttp80) cc_final: 0.7125 (ptm-80) REVERT: C 276 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.6679 (ptpt) REVERT: C 300 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7355 (tm-30) REVERT: C 336 GLU cc_start: 0.7941 (tp30) cc_final: 0.7443 (mm-30) REVERT: C 375 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7562 (tm-30) REVERT: C 464 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7474 (mt) REVERT: C 517 LYS cc_start: 0.8026 (tttt) cc_final: 0.7816 (tttm) REVERT: C 546 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6478 (tt0) REVERT: C 547 ARG cc_start: 0.7598 (ttm110) cc_final: 0.7022 (ttt90) REVERT: C 563 PHE cc_start: 0.8220 (t80) cc_final: 0.7931 (t80) REVERT: C 567 MET cc_start: 0.7230 (mmm) cc_final: 0.6648 (mmm) REVERT: D 49 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8179 (tt0) REVERT: D 62 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.5969 (mm-30) REVERT: D 75 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7863 (tt) REVERT: D 206 GLN cc_start: 0.7237 (mm-40) cc_final: 0.6800 (pt0) REVERT: D 248 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7146 (mm-30) REVERT: D 466 LYS cc_start: 0.7368 (mmmt) cc_final: 0.6022 (mppt) REVERT: E 81 ARG cc_start: 0.7546 (mtm-85) cc_final: 0.7259 (mpt-90) REVERT: E 109 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6609 (tp30) REVERT: E 209 GLU cc_start: 0.7813 (tt0) cc_final: 0.7485 (mm-30) REVERT: E 336 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7465 (pm20) REVERT: E 345 ARG cc_start: 0.7513 (ttm-80) cc_final: 0.6825 (mtm-85) REVERT: E 410 ARG cc_start: 0.6151 (mtm110) cc_final: 0.5736 (tpp80) REVERT: E 470 ILE cc_start: 0.1906 (OUTLIER) cc_final: 0.1520 (pt) REVERT: F 3 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6147 (tp) REVERT: F 6 LYS cc_start: 0.7239 (ttpp) cc_final: 0.6901 (ptpt) REVERT: F 46 GLN cc_start: 0.9107 (tt0) cc_final: 0.8885 (tt0) REVERT: F 88 MET cc_start: 0.9022 (mtm) cc_final: 0.8811 (mtt) REVERT: F 162 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7632 (mp0) REVERT: F 178 SER cc_start: 0.8292 (t) cc_final: 0.7911 (p) REVERT: F 305 LYS cc_start: 0.7958 (mttt) cc_final: 0.7157 (mmmt) REVERT: F 388 ASN cc_start: 0.7738 (OUTLIER) cc_final: 0.7225 (m110) REVERT: G 200 LYS cc_start: 0.7017 (mmmt) cc_final: 0.6498 (mmtt) REVERT: H 95 ARG cc_start: 0.6090 (OUTLIER) cc_final: 0.5825 (tmt170) REVERT: H 103 LYS cc_start: 0.6824 (OUTLIER) cc_final: 0.6448 (tmmm) REVERT: I 104 MET cc_start: 0.4582 (mtm) cc_final: 0.4038 (tmm) REVERT: J 110 GLU cc_start: 0.5714 (OUTLIER) cc_final: 0.5479 (tp30) REVERT: K 104 MET cc_start: 0.5464 (OUTLIER) cc_final: 0.4261 (mpp) REVERT: L 67 LEU cc_start: 0.5057 (OUTLIER) cc_final: 0.4611 (mm) REVERT: L 130 HIS cc_start: 0.4923 (OUTLIER) cc_final: 0.4388 (m90) outliers start: 138 outliers final: 63 residues processed: 460 average time/residue: 1.6167 time to fit residues: 866.9353 Evaluate side-chains 437 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 348 time to evaluate : 3.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 388 ASN Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 130 HIS Chi-restraints excluded: chain L residue 138 ARG Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 228 optimal weight: 0.6980 chunk 244 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 282 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN C 109 HIS C 283 HIS D 375 HIS D 407 ASN E 23 ASN E 338 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 30110 Z= 0.503 Angle : 0.703 9.349 40807 Z= 0.358 Chirality : 0.050 0.270 4572 Planarity : 0.006 0.055 5333 Dihedral : 6.604 93.648 4259 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.64 % Allowed : 18.59 % Favored : 76.78 % 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: 0.17 (0.14), residues: 3764 helix: 0.74 (0.13), residues: 1571 sheet: -0.40 (0.21), residues: 591 loop : -0.15 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP J 100 HIS 0.007 0.002 HIS F 344 PHE 0.025 0.003 PHE C 230 TYR 0.031 0.002 TYR A 439 ARG 0.011 0.001 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 348 time to evaluate : 3.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7864 (t70) cc_final: 0.7275 (t70) REVERT: A 92 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6543 (mp0) REVERT: A 104 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.6437 (mtp85) REVERT: A 130 ARG cc_start: 0.7653 (mtm110) cc_final: 0.6740 (ptt-90) REVERT: A 165 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: A 170 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6342 (mt-10) REVERT: A 261 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8080 (mm-30) REVERT: A 410 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7934 (m-30) REVERT: A 456 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7462 (tm-30) REVERT: A 481 ARG cc_start: 0.7639 (mtp85) cc_final: 0.6930 (ttp-110) REVERT: A 517 LYS cc_start: 0.7080 (tptp) cc_final: 0.6727 (tttt) REVERT: B 69 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7843 (mt) REVERT: B 122 MET cc_start: 0.7275 (mtt) cc_final: 0.6897 (mtp) REVERT: B 246 ASN cc_start: 0.7062 (t0) cc_final: 0.6742 (t0) REVERT: B 268 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6633 (tp30) REVERT: B 401 ARG cc_start: 0.7284 (mtp85) cc_final: 0.6799 (mtt-85) REVERT: B 435 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7648 (mp) REVERT: B 548 ILE cc_start: 0.6351 (mm) cc_final: 0.6135 (mm) REVERT: C 137 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8312 (m) REVERT: C 176 GLU cc_start: 0.6620 (mt-10) cc_final: 0.6293 (mt-10) REVERT: C 197 ARG cc_start: 0.7611 (ttp80) cc_final: 0.7121 (ptm-80) REVERT: C 276 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.6733 (ptpt) REVERT: C 300 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7376 (tm-30) REVERT: C 336 GLU cc_start: 0.7980 (tp30) cc_final: 0.7668 (tp30) REVERT: C 375 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7458 (tm-30) REVERT: C 517 LYS cc_start: 0.8048 (tttt) cc_final: 0.7820 (tttp) REVERT: C 546 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6681 (tt0) REVERT: C 547 ARG cc_start: 0.7707 (ttm110) cc_final: 0.7101 (ttt90) REVERT: C 563 PHE cc_start: 0.8370 (t80) cc_final: 0.8114 (t80) REVERT: C 567 MET cc_start: 0.7374 (mmm) cc_final: 0.6781 (mmm) REVERT: D 49 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: D 62 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.6077 (mm-30) REVERT: D 126 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7739 (ttpp) REVERT: D 206 GLN cc_start: 0.7295 (mm-40) cc_final: 0.6819 (pp30) REVERT: E 7 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: E 77 GLU cc_start: 0.8099 (pt0) cc_final: 0.7650 (pt0) REVERT: E 109 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6665 (tp30) REVERT: E 336 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7515 (pm20) REVERT: E 345 ARG cc_start: 0.7439 (ttm-80) cc_final: 0.6875 (mtm-85) REVERT: E 416 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.6950 (t70) REVERT: E 470 ILE cc_start: 0.1701 (OUTLIER) cc_final: 0.1493 (pt) REVERT: F 3 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.6159 (tp) REVERT: F 6 LYS cc_start: 0.7452 (ttpp) cc_final: 0.6986 (ptpt) REVERT: F 46 GLN cc_start: 0.9147 (tt0) cc_final: 0.8907 (tt0) REVERT: F 162 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7634 (mp0) REVERT: F 305 LYS cc_start: 0.8011 (mttt) cc_final: 0.7723 (mttp) REVERT: F 394 LYS cc_start: 0.7331 (mtmm) cc_final: 0.7121 (mttm) REVERT: G 13 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8181 (tm-30) REVERT: H 95 ARG cc_start: 0.6114 (OUTLIER) cc_final: 0.5778 (tmt170) REVERT: H 103 LYS cc_start: 0.6852 (OUTLIER) cc_final: 0.5449 (tptt) REVERT: J 119 LYS cc_start: 0.6522 (tttt) cc_final: 0.5585 (pptt) REVERT: K 104 MET cc_start: 0.5374 (OUTLIER) cc_final: 0.3947 (mpp) REVERT: L 67 LEU cc_start: 0.5170 (OUTLIER) cc_final: 0.4634 (mm) REVERT: L 130 HIS cc_start: 0.4821 (OUTLIER) cc_final: 0.4467 (m90) REVERT: L 150 LEU cc_start: 0.6457 (mt) cc_final: 0.6236 (mm) outliers start: 143 outliers final: 69 residues processed: 449 average time/residue: 1.5240 time to fit residues: 792.9975 Evaluate side-chains 431 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 334 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 126 LYS Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 394 LYS Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 130 HIS Chi-restraints excluded: chain L residue 138 ARG Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 160 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 0.8980 chunk 344 optimal weight: 2.9990 chunk 314 optimal weight: 2.9990 chunk 335 optimal weight: 10.0000 chunk 201 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 chunk 263 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 302 optimal weight: 0.6980 chunk 316 optimal weight: 0.8980 chunk 333 optimal weight: 0.0170 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN C 109 HIS D 407 ASN E 23 ASN E 338 GLN F 23 ASN F 388 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30110 Z= 0.179 Angle : 0.545 11.779 40807 Z= 0.271 Chirality : 0.043 0.150 4572 Planarity : 0.005 0.047 5333 Dihedral : 6.126 95.042 4259 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.11 % Allowed : 20.21 % Favored : 76.68 % 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: 0.59 (0.14), residues: 3764 helix: 1.14 (0.13), residues: 1570 sheet: -0.29 (0.21), residues: 588 loop : 0.06 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 100 HIS 0.002 0.001 HIS A 185 PHE 0.013 0.001 PHE E 130 TYR 0.019 0.001 TYR A 439 ARG 0.013 0.000 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 352 time to evaluate : 3.530 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6382 (mp0) REVERT: A 98 THR cc_start: 0.7624 (m) cc_final: 0.7322 (p) REVERT: A 104 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.6360 (mtp85) REVERT: A 115 LYS cc_start: 0.8072 (ttmp) cc_final: 0.7815 (tttp) REVERT: A 130 ARG cc_start: 0.7660 (mtm110) cc_final: 0.6782 (ptt-90) REVERT: A 170 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6351 (mt-10) REVERT: A 261 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8058 (mm-30) REVERT: A 449 GLU cc_start: 0.8080 (mp0) cc_final: 0.7817 (mp0) REVERT: A 456 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: A 481 ARG cc_start: 0.7566 (mtp85) cc_final: 0.6890 (ttp-170) REVERT: A 517 LYS cc_start: 0.7032 (tptp) cc_final: 0.6724 (tttt) REVERT: B 122 MET cc_start: 0.7236 (mtt) cc_final: 0.6892 (mtp) REVERT: B 133 MET cc_start: 0.7731 (mtp) cc_final: 0.7473 (mtp) REVERT: B 246 ASN cc_start: 0.6983 (t0) cc_final: 0.6717 (t0) REVERT: B 268 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6664 (tp30) REVERT: B 401 ARG cc_start: 0.7272 (mtp85) cc_final: 0.6769 (mtt-85) REVERT: B 435 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7623 (mp) REVERT: B 470 LEU cc_start: 0.7533 (tt) cc_final: 0.7179 (tp) REVERT: B 476 LEU cc_start: 0.7092 (mt) cc_final: 0.6779 (mm) REVERT: C 137 THR cc_start: 0.8706 (t) cc_final: 0.8308 (m) REVERT: C 197 ARG cc_start: 0.7561 (ttp80) cc_final: 0.7103 (ptm-80) REVERT: C 276 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.6640 (ptpt) REVERT: C 300 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: C 336 GLU cc_start: 0.7887 (tp30) cc_final: 0.7403 (mm-30) REVERT: C 517 LYS cc_start: 0.8026 (tttt) cc_final: 0.7809 (tttm) REVERT: C 547 ARG cc_start: 0.7636 (ttm110) cc_final: 0.7059 (ttt90) REVERT: C 563 PHE cc_start: 0.8256 (t80) cc_final: 0.7992 (t80) REVERT: C 567 MET cc_start: 0.7212 (mmm) cc_final: 0.6627 (mmm) REVERT: D 49 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: D 62 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.5918 (mm-30) REVERT: D 75 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7653 (tp) REVERT: D 206 GLN cc_start: 0.7296 (mm-40) cc_final: 0.6850 (pt0) REVERT: E 109 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6597 (tp30) REVERT: E 209 GLU cc_start: 0.7896 (tt0) cc_final: 0.7541 (mm-30) REVERT: E 336 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7487 (pm20) REVERT: E 345 ARG cc_start: 0.7458 (ttm-80) cc_final: 0.6921 (mtm-85) REVERT: E 410 ARG cc_start: 0.6098 (mtm110) cc_final: 0.5608 (tpp80) REVERT: E 416 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.6988 (t70) REVERT: F 3 LEU cc_start: 0.6448 (tp) cc_final: 0.6101 (tp) REVERT: F 6 LYS cc_start: 0.7302 (ttpp) cc_final: 0.6877 (ptpt) REVERT: F 46 GLN cc_start: 0.9090 (tt0) cc_final: 0.8843 (tt0) REVERT: F 162 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7603 (mp0) REVERT: F 178 SER cc_start: 0.8327 (t) cc_final: 0.7934 (p) REVERT: F 305 LYS cc_start: 0.8017 (mttt) cc_final: 0.7200 (mmmt) REVERT: F 345 ARG cc_start: 0.8181 (mmt90) cc_final: 0.7924 (mtt180) REVERT: G 13 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8174 (tm-30) REVERT: G 200 LYS cc_start: 0.7139 (mmmt) cc_final: 0.6578 (mmtt) REVERT: H 95 ARG cc_start: 0.6054 (OUTLIER) cc_final: 0.5832 (tmt170) REVERT: H 103 LYS cc_start: 0.6721 (OUTLIER) cc_final: 0.5334 (tptt) REVERT: I 104 MET cc_start: 0.4719 (tmm) cc_final: 0.4299 (mmm) REVERT: J 85 ARG cc_start: 0.4821 (ptp-110) cc_final: 0.4345 (mpt-90) REVERT: K 104 MET cc_start: 0.5234 (OUTLIER) cc_final: 0.3943 (mpp) REVERT: L 67 LEU cc_start: 0.4933 (OUTLIER) cc_final: 0.4428 (mm) REVERT: L 130 HIS cc_start: 0.4979 (OUTLIER) cc_final: 0.4515 (m90) outliers start: 96 outliers final: 50 residues processed: 424 average time/residue: 1.5838 time to fit residues: 780.3430 Evaluate side-chains 406 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 338 time to evaluate : 3.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 394 LYS Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 130 HIS Chi-restraints excluded: chain L residue 138 ARG Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 160 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 2.9990 chunk 354 optimal weight: 5.9990 chunk 216 optimal weight: 0.2980 chunk 168 optimal weight: 1.9990 chunk 246 optimal weight: 0.7980 chunk 371 optimal weight: 1.9990 chunk 342 optimal weight: 9.9990 chunk 295 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 228 optimal weight: 9.9990 chunk 181 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN C 109 HIS D 407 ASN E 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30110 Z= 0.241 Angle : 0.576 12.572 40807 Z= 0.285 Chirality : 0.044 0.235 4572 Planarity : 0.005 0.046 5333 Dihedral : 6.135 92.069 4259 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.08 % Allowed : 20.47 % Favored : 76.45 % 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: 3764 helix: 1.14 (0.13), residues: 1573 sheet: -0.30 (0.21), residues: 595 loop : 0.09 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 100 HIS 0.004 0.001 HIS F 344 PHE 0.016 0.001 PHE C 415 TYR 0.024 0.001 TYR A 439 ARG 0.011 0.000 ARG C 154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 342 time to evaluate : 3.814 Fit side-chains revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7207 (mt-10) REVERT: A 54 ASP cc_start: 0.7779 (t70) cc_final: 0.7244 (t70) REVERT: A 92 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6385 (mp0) REVERT: A 98 THR cc_start: 0.7668 (m) cc_final: 0.7361 (p) REVERT: A 104 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.6386 (mtp85) REVERT: A 115 LYS cc_start: 0.8114 (ttmp) cc_final: 0.7853 (tttp) REVERT: A 130 ARG cc_start: 0.7668 (mtm110) cc_final: 0.6775 (ptt-90) REVERT: A 170 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6359 (mt-10) REVERT: A 261 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8056 (mm-30) REVERT: A 449 GLU cc_start: 0.8084 (mp0) cc_final: 0.7817 (mp0) REVERT: A 481 ARG cc_start: 0.7582 (mtp85) cc_final: 0.6891 (ttp-110) REVERT: A 517 LYS cc_start: 0.7029 (tptp) cc_final: 0.6725 (tttt) REVERT: B 122 MET cc_start: 0.7242 (mtt) cc_final: 0.6883 (mtp) REVERT: B 133 MET cc_start: 0.7719 (mtp) cc_final: 0.7383 (mtp) REVERT: B 246 ASN cc_start: 0.6959 (t0) cc_final: 0.6755 (t0) REVERT: B 268 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6641 (tp30) REVERT: B 401 ARG cc_start: 0.7280 (mtp85) cc_final: 0.6780 (mtt-85) REVERT: B 435 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7656 (mp) REVERT: C 137 THR cc_start: 0.8675 (t) cc_final: 0.8270 (m) REVERT: C 197 ARG cc_start: 0.7617 (ttp80) cc_final: 0.7149 (ptm-80) REVERT: C 276 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.6635 (ptpt) REVERT: C 300 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: C 336 GLU cc_start: 0.7903 (tp30) cc_final: 0.7427 (mm-30) REVERT: C 547 ARG cc_start: 0.7684 (ttm110) cc_final: 0.7059 (ttt90) REVERT: C 563 PHE cc_start: 0.8257 (t80) cc_final: 0.7989 (t80) REVERT: C 567 MET cc_start: 0.7273 (mmm) cc_final: 0.6671 (mmm) REVERT: D 49 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: D 62 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.5931 (mm-30) REVERT: D 75 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7652 (tp) REVERT: D 206 GLN cc_start: 0.7277 (mm-40) cc_final: 0.6833 (pt0) REVERT: E 109 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6630 (tp30) REVERT: E 336 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.7534 (pm20) REVERT: E 345 ARG cc_start: 0.7429 (ttm-80) cc_final: 0.6915 (mtm-85) REVERT: E 410 ARG cc_start: 0.6121 (mtm110) cc_final: 0.5748 (tpp80) REVERT: E 416 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.6960 (t70) REVERT: E 448 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.7033 (mt0) REVERT: F 3 LEU cc_start: 0.6463 (tp) cc_final: 0.6135 (tp) REVERT: F 6 LYS cc_start: 0.7306 (ttpp) cc_final: 0.6900 (ptpt) REVERT: F 46 GLN cc_start: 0.9102 (tt0) cc_final: 0.8861 (tt0) REVERT: F 86 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7687 (ttmt) REVERT: F 162 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7612 (mp0) REVERT: F 305 LYS cc_start: 0.8034 (mttt) cc_final: 0.7224 (mmmt) REVERT: G 13 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8209 (tm-30) REVERT: G 200 LYS cc_start: 0.7010 (mmmt) cc_final: 0.6437 (mmtt) REVERT: H 95 ARG cc_start: 0.6120 (OUTLIER) cc_final: 0.5872 (tmt170) REVERT: H 103 LYS cc_start: 0.6710 (OUTLIER) cc_final: 0.6269 (tmmm) REVERT: J 85 ARG cc_start: 0.4813 (ptp-110) cc_final: 0.4341 (mpt-90) REVERT: J 112 LEU cc_start: 0.3643 (OUTLIER) cc_final: 0.3093 (tm) REVERT: K 104 MET cc_start: 0.5228 (OUTLIER) cc_final: 0.3931 (mpp) REVERT: L 67 LEU cc_start: 0.4975 (OUTLIER) cc_final: 0.4476 (mm) REVERT: L 128 LEU cc_start: 0.5240 (pp) cc_final: 0.4749 (tt) REVERT: L 130 HIS cc_start: 0.4950 (OUTLIER) cc_final: 0.4517 (m90) outliers start: 95 outliers final: 58 residues processed: 412 average time/residue: 1.5833 time to fit residues: 755.0251 Evaluate side-chains 414 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 335 time to evaluate : 3.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 394 LYS Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 130 HIS Chi-restraints excluded: chain L residue 138 ARG Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 160 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 0.0770 chunk 315 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 272 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 296 optimal weight: 0.5980 chunk 124 optimal weight: 0.1980 chunk 304 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN C 3 GLN C 109 HIS D 407 ASN E 23 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.156493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.122527 restraints weight = 37798.070| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.69 r_work: 0.3197 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30110 Z= 0.207 Angle : 0.556 13.914 40807 Z= 0.273 Chirality : 0.043 0.189 4572 Planarity : 0.005 0.047 5333 Dihedral : 6.009 90.362 4259 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.92 % Allowed : 20.69 % Favored : 76.39 % 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: 3764 helix: 1.20 (0.13), residues: 1571 sheet: -0.27 (0.21), residues: 595 loop : 0.14 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 100 HIS 0.003 0.001 HIS B 145 PHE 0.014 0.001 PHE C 415 TYR 0.022 0.001 TYR A 439 ARG 0.014 0.000 ARG C 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13792.03 seconds wall clock time: 243 minutes 42.97 seconds (14622.97 seconds total)