Starting phenix.real_space_refine on Wed Feb 21 03:41:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vay_31871/02_2024/7vay_31871_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vay_31871/02_2024/7vay_31871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vay_31871/02_2024/7vay_31871.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vay_31871/02_2024/7vay_31871.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vay_31871/02_2024/7vay_31871_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vay_31871/02_2024/7vay_31871_updated.pdb" } resolution = 3.3 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 105 5.16 5 C 18735 2.51 5 N 5131 2.21 5 O 5572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 441": "OE1" <-> "OE2" Residue "C TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 296": "OE1" <-> "OE2" Residue "F TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s 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: 16 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: {'CIS': 1, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 441} 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: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.50, per 1000 atoms: 0.59 Number of scatterers: 29553 At special positions: 0 Unit cell: (149.04, 144.18, 171.72, 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 105 16.00 P 8 15.00 Mg 2 11.99 O 5572 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.94 Conformation dependent library (CDL) restraints added in 5.8 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: 133 helices and 37 sheets defined 42.3% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.04 Creating SS restraints... Processing helix chain 'A' and resid 91 through 98 Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 259 through 271 Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 296 through 316 removed outlier: 4.086A pdb=" N GLU A 300 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 341 Processing helix chain 'A' and resid 352 through 364 removed outlier: 4.098A pdb=" N ALA A 355 " --> pdb=" O PRO A 352 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 363 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 364 " --> pdb=" O PHE A 361 " (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 400 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 447 through 471 removed outlier: 3.833A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) 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: 3.600A pdb=" N GLN A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 4.468A pdb=" N ARG A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N TYR A 553 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 576 Processing helix chain 'B' and resid 91 through 98 removed outlier: 3.599A pdb=" N LYS B 97 " --> pdb=" O ARG B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 259 through 271 Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 296 through 316 removed outlier: 4.631A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 316 " --> pdb=" O TYR B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 Processing helix chain 'B' and resid 354 through 364 removed outlier: 3.976A pdb=" N ARG B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 432 through 442 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 447 through 463 Processing helix chain 'B' and resid 465 through 470 Processing helix chain 'B' and resid 478 through 493 Processing helix chain 'B' and resid 509 through 532 Processing helix chain 'B' and resid 536 through 541 removed outlier: 3.508A pdb=" N GLN B 541 " --> pdb=" O ASP B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.540A pdb=" N ARG B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR B 553 " --> pdb=" O GLY B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 576 Proline residue: B 560 - end of helix Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 259 through 271 Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 282 through 284 No H-bonds generated for 'chain 'C' and resid 282 through 284' Processing helix chain 'C' and resid 296 through 316 removed outlier: 4.014A pdb=" N GLU C 300 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 340 Processing helix chain 'C' and resid 354 through 364 removed outlier: 3.959A pdb=" N ARG C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 394 through 400 Processing helix chain 'C' and resid 411 through 416 Processing helix chain 'C' and resid 436 through 442 Processing helix chain 'C' and resid 447 through 471 removed outlier: 4.154A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.116A 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 494 Processing helix chain 'C' and resid 509 through 531 Processing helix chain 'C' and resid 536 through 539 No H-bonds generated for 'chain 'C' and resid 536 through 539' Processing helix chain 'C' and resid 543 through 553 removed outlier: 4.087A pdb=" N ARG C 552 " --> 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: 3.641A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 176 through 178 No H-bonds generated for 'chain 'D' and resid 176 through 178' Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 213 through 216 Processing helix chain 'D' and resid 228 through 249 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 287 through 297 removed outlier: 4.298A pdb=" N ARG D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 362 through 365 No H-bonds generated for 'chain 'D' and resid 362 through 365' Processing helix chain 'D' and resid 375 through 399 removed outlier: 3.837A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 421 Processing helix chain 'D' and resid 432 through 445 removed outlier: 3.825A 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 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 136 through 139 No H-bonds generated for 'chain 'E' and resid 136 through 139' Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 198 through 209 Processing helix chain 'E' and resid 213 through 216 Processing helix chain 'E' and resid 228 through 249 removed outlier: 3.808A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 260 through 274 Processing helix chain 'E' and resid 287 through 297 removed outlier: 4.635A 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 345 Processing helix chain 'E' and resid 360 through 364 removed outlier: 4.405A pdb=" N ASN E 363 " --> pdb=" O ARG E 360 " (cutoff:3.500A) removed outlier: 3.697A 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: 3.682A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 421 Processing helix chain 'E' and resid 432 through 442 Processing helix chain 'E' and resid 459 through 462 No H-bonds generated for 'chain 'E' and resid 459 through 462' Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.522A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY F 90 " --> pdb=" O GLU F 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 86 through 90' Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 160 through 170 Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 198 through 211 Processing helix chain 'F' and resid 213 through 216 Processing helix chain 'F' and resid 228 through 249 removed outlier: 3.691A pdb=" N THR F 234 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.543A pdb=" N PHE F 247 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N HIS F 249 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 274 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: 4.164A pdb=" N TYR F 288 " --> pdb=" O GLY F 285 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLU F 296 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG F 297 " --> pdb=" O ILE F 294 " (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 360 through 365 removed outlier: 4.390A pdb=" N ASN F 363 " --> pdb=" O ARG F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 399 removed outlier: 3.802A 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: 3.795A pdb=" N MET F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 450 No H-bonds generated for 'chain 'F' and resid 448 through 450' Processing helix chain 'F' and resid 456 through 462 Processing helix chain 'F' and resid 467 through 470 No H-bonds generated for 'chain 'F' and resid 467 through 470' Processing helix chain 'G' and resid 8 through 70 removed outlier: 3.601A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (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 208 removed outlier: 4.860A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 7 through 16 removed outlier: 3.801A pdb=" N ALA H 16 " --> pdb=" O GLY H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 39 Processing helix chain 'H' and resid 55 through 59 removed outlier: 3.635A pdb=" N VAL H 59 " --> pdb=" O GLU H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 82 removed outlier: 3.979A pdb=" N GLN H 82 " --> pdb=" O LYS H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 97 Processing helix chain 'I' and resid 82 through 118 removed outlier: 4.029A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASP I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLU I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 91 Processing helix chain 'J' and resid 98 through 114 Proline residue: J 101 - end of helix removed outlier: 3.506A pdb=" N VAL J 104 " --> pdb=" O PRO J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 130 Proline residue: J 129 - end of helix No H-bonds generated for 'chain 'J' and resid 125 through 130' Processing helix chain 'J' and resid 133 through 138 Processing helix chain 'J' and resid 167 through 186 removed outlier: 4.394A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 106 removed outlier: 3.664A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 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 100 through 114 Processing helix chain 'L' and resid 125 through 138 Proline residue: L 129 - end of helix removed outlier: 3.962A pdb=" N GLU L 132 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ALA L 133 " --> pdb=" O HIS L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 186 removed outlier: 5.540A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.445A 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: 3.813A pdb=" N ILE A 2 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ILE A 6 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 75 Processing sheet with id= C, first strand: chain 'A' and resid 117 through 119 Processing sheet with id= D, first strand: chain 'A' and resid 223 through 227 removed outlier: 8.424A pdb=" N ALA A 224 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE A 380 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE A 226 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLY A 382 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 249 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N MET A 323 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 251 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 366 through 369 Processing sheet with id= F, first strand: chain 'A' and resid 134 through 139 removed outlier: 6.630A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 157 through 160 removed outlier: 6.940A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.979A pdb=" N ILE B 2 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.400A 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 117 through 119 Processing sheet with id= K, first strand: chain 'B' and resid 405 through 407 removed outlier: 8.738A pdb=" N ALA B 224 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE B 380 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ILE B 226 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY B 382 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL B 249 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N MET B 323 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL B 251 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 366 through 369 removed outlier: 3.523A pdb=" N VAL B 378 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 134 through 139 removed outlier: 6.663A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 157 through 160 removed outlier: 6.821A 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: 6.713A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ILE C 6 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 72 through 75 Processing sheet with id= Q, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.084A pdb=" N GLY C 82 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA C 324 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL C 381 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 3.515A 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 120 removed outlier: 3.818A pdb=" N GLY C 164 " --> pdb=" O TRP C 119 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 197 through 199 removed outlier: 3.557A pdb=" N ARG C 197 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS C 367 " --> pdb=" O LEU C 199 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 134 through 139 removed outlier: 6.642A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.514A 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: 6.661A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL C 160 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL C 172 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU C 181 " --> pdb=" O VAL C 172 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 11 through 15 removed outlier: 6.375A pdb=" N PHE D 20 " --> pdb=" O THR D 12 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE D 14 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU D 18 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 77 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASP D 34 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU D 75 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LYS D 36 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.056A 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: 3.599A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.868A pdb=" N ARG D 91 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N HIS D 252 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL D 190 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU D 254 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ALA D 192 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE D 256 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N SER D 307 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL D 255 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR D 309 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE D 311 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 336 through 338 Processing sheet with id= Z, first strand: chain 'E' and resid 11 through 15 removed outlier: 6.433A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.190A 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 336 through 338 Processing sheet with id= AC, first strand: chain 'E' and resid 217 through 220 removed outlier: 8.749A pdb=" N VAL E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N HIS E 252 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL E 190 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU E 254 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA E 192 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE E 256 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU E 257 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE E 311 " --> pdb=" O LEU E 257 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'F' and resid 11 through 15 removed outlier: 6.414A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ASP F 34 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU F 75 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LYS F 36 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.323A 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 92 through 94 removed outlier: 7.853A pdb=" N PHE F 93 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU F 219 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N SER F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL F 255 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR F 309 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE F 311 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 336 through 338 Processing sheet with id= AH, first strand: chain 'G' and resid 89 through 96 Processing sheet with id= AI, first strand: chain 'H' and resid 19 through 22 removed outlier: 6.515A pdb=" N VAL H 70 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL H 47 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.604A 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: 3.733A pdb=" N GLU J 141 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL J 155 " --> pdb=" O LYS J 119 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU J 121 " --> pdb=" O ARG J 153 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG J 153 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'L' and resid 120 through 122 removed outlier: 3.925A pdb=" N ALA L 120 " --> pdb=" O VAL L 155 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL L 155 " --> pdb=" O ALA L 120 " (cutoff:3.500A) 1224 hydrogen bonds defined for protein. 3315 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.07 Time building geometry restraints manager: 12.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 10094 1.37 - 1.51: 9463 1.51 - 1.66: 10357 1.66 - 1.80: 188 1.80 - 1.95: 8 Bond restraints: 30110 Sorted by residual: bond pdb=" C4 ADP A 602 " pdb=" C5 ADP A 602 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C5 ADP A 602 " pdb=" C6 ADP A 602 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C HIS C 418 " pdb=" N PHE C 419 " ideal model delta sigma weight residual 1.327 1.273 0.054 1.71e-02 3.42e+03 9.87e+00 bond pdb=" O3B ADP A 602 " pdb=" PB ADP A 602 " ideal model delta sigma weight residual 1.510 1.572 -0.062 2.00e-02 2.50e+03 9.75e+00 bond pdb=" CA GLU D 296 " pdb=" C GLU D 296 " ideal model delta sigma weight residual 1.522 1.489 0.033 1.38e-02 5.25e+03 5.76e+00 ... (remaining 30105 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.54: 1035 106.54 - 113.40: 16397 113.40 - 120.26: 11073 120.26 - 127.13: 11984 127.13 - 133.99: 318 Bond angle restraints: 40807 Sorted by residual: angle pdb=" O2B ADP A 602 " pdb=" PB ADP A 602 " pdb=" O3B ADP A 602 " ideal model delta sigma weight residual 119.90 105.58 14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" N ILE D 100 " pdb=" CA ILE D 100 " pdb=" C ILE D 100 " ideal model delta sigma weight residual 113.20 109.54 3.66 9.60e-01 1.09e+00 1.45e+01 angle pdb=" N ILE E 100 " pdb=" CA ILE E 100 " pdb=" C ILE E 100 " ideal model delta sigma weight residual 113.20 109.96 3.24 9.60e-01 1.09e+00 1.14e+01 angle pdb=" N ILE D 96 " pdb=" CA ILE D 96 " pdb=" C ILE D 96 " ideal model delta sigma weight residual 111.88 108.45 3.43 1.06e+00 8.90e-01 1.05e+01 angle pdb=" CA LEU L 148 " pdb=" CB LEU L 148 " pdb=" CG LEU L 148 " ideal model delta sigma weight residual 116.30 127.27 -10.97 3.50e+00 8.16e-02 9.82e+00 ... (remaining 40802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.88: 17532 24.88 - 49.76: 701 49.76 - 74.63: 85 74.63 - 99.51: 36 99.51 - 124.39: 1 Dihedral angle restraints: 18355 sinusoidal: 7533 harmonic: 10822 Sorted by residual: dihedral pdb=" C5' ADP A 602 " pdb=" O5' ADP A 602 " pdb=" PA ADP A 602 " pdb=" O2A ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 64.39 -124.39 1 2.00e+01 2.50e-03 3.76e+01 dihedral pdb=" CA ARG K 87 " pdb=" C ARG K 87 " pdb=" N TYR K 88 " pdb=" CA TYR K 88 " ideal model delta harmonic sigma weight residual 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" O2A ADP A 602 " pdb=" O3A ADP A 602 " pdb=" PA ADP A 602 " pdb=" PB ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 -129.64 69.64 1 2.00e+01 2.50e-03 1.57e+01 ... (remaining 18352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2991 0.035 - 0.071: 1027 0.071 - 0.106: 432 0.106 - 0.142: 119 0.142 - 0.177: 7 Chirality restraints: 4576 Sorted by residual: chirality pdb=" C2' ADP A 602 " pdb=" C1' ADP A 602 " pdb=" C3' ADP A 602 " pdb=" O2' ADP A 602 " both_signs ideal model delta sigma weight residual False -2.51 -2.69 0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" CA ARG K 87 " pdb=" N ARG K 87 " pdb=" C ARG K 87 " pdb=" CB ARG K 87 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.64e-01 chirality pdb=" CA PHE B 269 " pdb=" N PHE B 269 " pdb=" C PHE B 269 " pdb=" CB PHE B 269 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.09e-01 ... (remaining 4573 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO E 324 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 277 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO E 278 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO E 278 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 278 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 323 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO F 324 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO F 324 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 324 " 0.024 5.00e-02 4.00e+02 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 200 2.54 - 3.13: 23220 3.13 - 3.72: 47411 3.72 - 4.31: 66371 4.31 - 4.90: 112017 Nonbonded interactions: 249219 Sorted by model distance: nonbonded pdb=" OG SER C 235 " pdb="MG MG C 601 " model vdw 1.949 2.170 nonbonded pdb=" OE2 GLU G 59 " pdb=" NH2 ARG G 132 " model vdw 2.062 2.520 nonbonded pdb=" OH TYR E 411 " pdb=" OE1 GLU E 450 " model vdw 2.107 2.440 nonbonded pdb=" OH TYR F 263 " pdb=" OD2 ASP F 290 " model vdw 2.110 2.440 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 2.140 2.440 ... (remaining 249214 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: 4.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 15.920 Check model and map are aligned: 0.500 Set scattering table: 0.310 Process input model: 82.600 Find NCS groups from input model: 2.110 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: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 30110 Z= 0.297 Angle : 0.585 14.315 40807 Z= 0.309 Chirality : 0.044 0.177 4576 Planarity : 0.004 0.045 5333 Dihedral : 13.655 124.388 11437 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.14), residues: 3764 helix: 1.53 (0.14), residues: 1545 sheet: -0.29 (0.23), residues: 534 loop : 0.43 (0.16), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 471 HIS 0.003 0.001 HIS A 418 PHE 0.021 0.001 PHE B 269 TYR 0.015 0.001 TYR D 463 ARG 0.006 0.000 ARG G 132 *********************** 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 639 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 639 time to evaluate : 3.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8146 (mm) cc_final: 0.7872 (mt) REVERT: A 8 LYS cc_start: 0.7634 (ttmt) cc_final: 0.7273 (tttt) REVERT: A 124 LYS cc_start: 0.7447 (mtmm) cc_final: 0.7084 (mmtt) REVERT: A 180 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7635 (mt-10) REVERT: A 311 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 323 MET cc_start: 0.7563 (mpp) cc_final: 0.7271 (mmt) REVERT: A 340 ARG cc_start: 0.7231 (mmt180) cc_final: 0.6927 (mmm160) REVERT: A 408 ARG cc_start: 0.7433 (ttt180) cc_final: 0.7219 (ttm-80) REVERT: A 452 ASP cc_start: 0.7000 (m-30) cc_final: 0.6272 (m-30) REVERT: A 491 ARG cc_start: 0.7384 (mtm110) cc_final: 0.7183 (mtm110) REVERT: A 492 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7396 (mt-10) REVERT: A 527 GLU cc_start: 0.6926 (tt0) cc_final: 0.6690 (tt0) REVERT: A 537 ASP cc_start: 0.6948 (m-30) cc_final: 0.6673 (t70) REVERT: B 7 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7485 (tt0) REVERT: B 43 ASP cc_start: 0.7152 (t0) cc_final: 0.6891 (t70) REVERT: B 152 ASP cc_start: 0.6600 (p0) cc_final: 0.6302 (t70) REVERT: B 176 GLU cc_start: 0.6362 (mm-30) cc_final: 0.6006 (pm20) REVERT: B 271 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7450 (mt-10) REVERT: B 311 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6863 (mt-10) REVERT: B 348 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7491 (mm-30) REVERT: B 424 TRP cc_start: 0.6738 (p90) cc_final: 0.5883 (p90) REVERT: B 459 GLN cc_start: 0.6721 (tp-100) cc_final: 0.6355 (mm-40) REVERT: B 480 GLU cc_start: 0.6282 (mp0) cc_final: 0.5932 (mt-10) REVERT: B 509 MET cc_start: 0.5869 (mmm) cc_final: 0.5338 (mmm) REVERT: B 547 ARG cc_start: 0.4691 (tpp-160) cc_final: 0.4387 (tpp80) REVERT: B 550 ARG cc_start: 0.6385 (mmm160) cc_final: 0.5774 (mmp80) REVERT: B 558 GLU cc_start: 0.6446 (mt-10) cc_final: 0.6226 (tp30) REVERT: C 112 ASP cc_start: 0.8002 (t0) cc_final: 0.7737 (t70) REVERT: C 124 LYS cc_start: 0.8302 (mppt) cc_final: 0.7699 (mmtt) REVERT: C 161 LYS cc_start: 0.7789 (mmtp) cc_final: 0.7551 (mmtt) REVERT: C 267 VAL cc_start: 0.7584 (t) cc_final: 0.7073 (m) REVERT: C 343 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7814 (mt-10) REVERT: C 344 MET cc_start: 0.7974 (ttp) cc_final: 0.7297 (tpp) REVERT: C 408 ARG cc_start: 0.7115 (ttt180) cc_final: 0.6866 (ttt-90) REVERT: C 488 ARG cc_start: 0.7312 (tmm160) cc_final: 0.6470 (ttt90) REVERT: D 6 LYS cc_start: 0.8051 (tptp) cc_final: 0.7628 (tttm) REVERT: D 34 ASP cc_start: 0.7519 (m-30) cc_final: 0.7104 (p0) REVERT: D 74 SER cc_start: 0.8113 (p) cc_final: 0.7756 (t) REVERT: D 86 LYS cc_start: 0.7405 (mtpt) cc_final: 0.7171 (ttmt) REVERT: D 194 MET cc_start: 0.8777 (mtm) cc_final: 0.8573 (mtm) REVERT: D 203 TYR cc_start: 0.7851 (t80) cc_final: 0.7600 (t80) REVERT: D 264 CYS cc_start: 0.7686 (m) cc_final: 0.7123 (m) REVERT: D 338 GLN cc_start: 0.7967 (tt0) cc_final: 0.7641 (tt0) REVERT: D 368 LYS cc_start: 0.8043 (mtmt) cc_final: 0.7591 (mtmm) REVERT: D 377 GLN cc_start: 0.7181 (mt0) cc_final: 0.6777 (mm-40) REVERT: D 398 ILE cc_start: 0.7738 (pt) cc_final: 0.7502 (mt) REVERT: D 416 ASP cc_start: 0.7648 (t0) cc_final: 0.6872 (m-30) REVERT: D 428 GLN cc_start: 0.7457 (mt0) cc_final: 0.7114 (mt0) REVERT: E 79 VAL cc_start: 0.7888 (t) cc_final: 0.7685 (p) REVERT: E 186 PRO cc_start: 0.7081 (Cg_exo) cc_final: 0.6832 (Cg_endo) REVERT: E 206 GLN cc_start: 0.7289 (tm-30) cc_final: 0.6823 (pt0) REVERT: E 207 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6578 (mm-30) REVERT: E 250 ASP cc_start: 0.7692 (m-30) cc_final: 0.6700 (t0) REVERT: E 260 MET cc_start: 0.8317 (mmm) cc_final: 0.7706 (mmm) REVERT: E 315 SER cc_start: 0.8027 (m) cc_final: 0.7788 (p) REVERT: E 362 MET cc_start: 0.7763 (ttt) cc_final: 0.7462 (ttp) REVERT: E 376 LYS cc_start: 0.6835 (ttpt) cc_final: 0.6583 (ttmm) REVERT: E 393 ARG cc_start: 0.5729 (ptp-170) cc_final: 0.5401 (ptp-170) REVERT: E 421 PHE cc_start: 0.6745 (m-80) cc_final: 0.6143 (m-80) REVERT: E 440 TRP cc_start: 0.6539 (m100) cc_final: 0.6268 (m100) REVERT: E 450 GLU cc_start: 0.6050 (mm-30) cc_final: 0.5335 (mt-10) REVERT: F 22 GLU cc_start: 0.7952 (pt0) cc_final: 0.7671 (pt0) REVERT: F 25 LYS cc_start: 0.8246 (ptmm) cc_final: 0.7852 (ptmt) REVERT: F 52 GLU cc_start: 0.7539 (pt0) cc_final: 0.7218 (mt-10) REVERT: F 128 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6955 (mt-10) REVERT: F 264 CYS cc_start: 0.8098 (m) cc_final: 0.7704 (m) REVERT: F 318 ASP cc_start: 0.6354 (p0) cc_final: 0.5807 (t0) REVERT: F 340 SER cc_start: 0.8389 (t) cc_final: 0.7762 (p) REVERT: F 406 GLU cc_start: 0.7165 (tp30) cc_final: 0.6553 (mm-30) REVERT: G 6 PRO cc_start: 0.8161 (Cg_endo) cc_final: 0.7904 (Cg_exo) REVERT: G 13 GLN cc_start: 0.7173 (tm-30) cc_final: 0.6493 (tm-30) REVERT: G 44 ARG cc_start: 0.7350 (mtp180) cc_final: 0.6941 (ttm170) REVERT: G 145 THR cc_start: 0.7834 (t) cc_final: 0.7587 (p) REVERT: G 184 GLU cc_start: 0.7096 (tt0) cc_final: 0.6771 (tp30) REVERT: G 187 GLU cc_start: 0.6816 (tt0) cc_final: 0.6602 (tt0) REVERT: H 18 LEU cc_start: 0.3588 (mm) cc_final: 0.2868 (tt) REVERT: H 71 LEU cc_start: 0.6443 (pp) cc_final: 0.6100 (pt) REVERT: H 90 MET cc_start: 0.6084 (tpp) cc_final: 0.5422 (tpp) REVERT: J 65 GLU cc_start: 0.3383 (tp30) cc_final: 0.3103 (tp30) REVERT: J 70 THR cc_start: 0.5159 (m) cc_final: 0.4956 (m) REVERT: J 78 GLU cc_start: 0.6113 (tp30) cc_final: 0.5625 (mt-10) REVERT: J 82 GLU cc_start: 0.5756 (mm-30) cc_final: 0.5298 (mt-10) REVERT: J 103 VAL cc_start: 0.5950 (m) cc_final: 0.5727 (p) REVERT: J 113 GLU cc_start: 0.6754 (tm-30) cc_final: 0.6427 (pt0) REVERT: L 65 GLU cc_start: 0.5057 (pp20) cc_final: 0.3996 (tp30) REVERT: L 67 LEU cc_start: 0.6106 (pp) cc_final: 0.5398 (tp) REVERT: L 81 GLU cc_start: 0.7153 (pp20) cc_final: 0.5878 (mm-30) REVERT: L 82 GLU cc_start: 0.5948 (tp30) cc_final: 0.4990 (tt0) REVERT: L 88 ARG cc_start: 0.6419 (mtp-110) cc_final: 0.5914 (tmm-80) REVERT: L 109 LEU cc_start: 0.7083 (pp) cc_final: 0.6276 (mt) REVERT: L 141 GLU cc_start: 0.5950 (tt0) cc_final: 0.5565 (tp30) REVERT: L 173 ARG cc_start: 0.6339 (mmm-85) cc_final: 0.4976 (ttt180) outliers start: 0 outliers final: 0 residues processed: 639 average time/residue: 0.5135 time to fit residues: 481.7977 Evaluate side-chains 373 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 3.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 10.0000 chunk 282 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 190 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 292 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 217 optimal weight: 10.0000 chunk 338 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS B 81 ASN C 571 GLN D 170 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 58 GLN E 129 GLN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN ** F 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 30110 Z= 0.549 Angle : 0.726 9.687 40807 Z= 0.369 Chirality : 0.051 0.201 4576 Planarity : 0.007 0.075 5333 Dihedral : 6.392 106.355 4231 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.13 % Rotamer: Outliers : 1.56 % Allowed : 9.28 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.22 (0.14), residues: 3764 helix: 0.70 (0.13), residues: 1570 sheet: -0.46 (0.21), residues: 594 loop : 0.01 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 424 HIS 0.006 0.001 HIS B 418 PHE 0.020 0.003 PHE A 205 TYR 0.024 0.002 TYR E 54 ARG 0.013 0.001 ARG E 210 *********************** 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 400 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 352 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7596 (ttmt) cc_final: 0.7054 (tttt) REVERT: A 43 ASP cc_start: 0.7158 (t0) cc_final: 0.6785 (t70) REVERT: A 122 MET cc_start: 0.8122 (mtp) cc_final: 0.7637 (ttm) REVERT: A 124 LYS cc_start: 0.7463 (mtmm) cc_final: 0.7109 (mmtt) REVERT: A 180 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7649 (mt-10) REVERT: A 323 MET cc_start: 0.8112 (mpp) cc_final: 0.7806 (mmt) REVERT: A 408 ARG cc_start: 0.7477 (ttt180) cc_final: 0.7240 (ttm-80) REVERT: A 469 GLN cc_start: 0.6748 (OUTLIER) cc_final: 0.6154 (mp10) REVERT: B 43 ASP cc_start: 0.7357 (t0) cc_final: 0.7088 (t70) REVERT: B 152 ASP cc_start: 0.6588 (p0) cc_final: 0.6164 (t70) REVERT: B 197 ARG cc_start: 0.7408 (ttp-110) cc_final: 0.6992 (ttp-170) REVERT: B 271 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7429 (mt-10) REVERT: B 459 GLN cc_start: 0.6656 (tp-100) cc_final: 0.6437 (mm-40) REVERT: B 480 GLU cc_start: 0.6266 (mp0) cc_final: 0.5926 (mt-10) REVERT: B 493 ASP cc_start: 0.6347 (m-30) cc_final: 0.5810 (t0) REVERT: B 513 TYR cc_start: 0.5612 (t80) cc_final: 0.5363 (t80) REVERT: B 547 ARG cc_start: 0.4754 (tpp-160) cc_final: 0.4434 (tpp80) REVERT: B 558 GLU cc_start: 0.6732 (mt-10) cc_final: 0.6416 (tp30) REVERT: C 112 ASP cc_start: 0.8395 (t0) cc_final: 0.8183 (t70) REVERT: C 124 LYS cc_start: 0.8301 (mppt) cc_final: 0.7747 (mmtt) REVERT: C 197 ARG cc_start: 0.7564 (ttp-110) cc_final: 0.7323 (mtm110) REVERT: C 344 MET cc_start: 0.7895 (ttp) cc_final: 0.7367 (tpp) REVERT: C 374 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6219 (mt-10) REVERT: C 564 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7206 (tp30) REVERT: D 6 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7538 (tttm) REVERT: D 34 ASP cc_start: 0.7717 (m-30) cc_final: 0.6976 (p0) REVERT: D 74 SER cc_start: 0.8337 (p) cc_final: 0.7356 (p) REVERT: D 86 LYS cc_start: 0.7378 (mtpt) cc_final: 0.7115 (ttmt) REVERT: D 98 LYS cc_start: 0.7255 (mttt) cc_final: 0.7007 (mmtt) REVERT: D 259 ASP cc_start: 0.7365 (t70) cc_final: 0.6950 (t70) REVERT: D 264 CYS cc_start: 0.7834 (m) cc_final: 0.7183 (m) REVERT: D 368 LYS cc_start: 0.8096 (mtmt) cc_final: 0.7668 (mtmm) REVERT: D 377 GLN cc_start: 0.7093 (mt0) cc_final: 0.6828 (mm-40) REVERT: D 394 LYS cc_start: 0.8043 (ttmm) cc_final: 0.7763 (mtpt) REVERT: D 398 ILE cc_start: 0.8011 (pt) cc_final: 0.7729 (mt) REVERT: E 186 PRO cc_start: 0.7017 (Cg_exo) cc_final: 0.6646 (Cg_endo) REVERT: E 206 GLN cc_start: 0.7400 (tm-30) cc_final: 0.6956 (pt0) REVERT: E 207 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6822 (mm-30) REVERT: E 209 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7832 (tm-30) REVERT: E 250 ASP cc_start: 0.7721 (m-30) cc_final: 0.6608 (t0) REVERT: E 260 MET cc_start: 0.7921 (mmm) cc_final: 0.7721 (mmm) REVERT: E 315 SER cc_start: 0.8314 (m) cc_final: 0.8012 (p) REVERT: E 353 ASP cc_start: 0.7598 (t0) cc_final: 0.6606 (p0) REVERT: E 362 MET cc_start: 0.7755 (ttt) cc_final: 0.7398 (ttp) REVERT: E 421 PHE cc_start: 0.7238 (m-80) cc_final: 0.6429 (m-80) REVERT: E 440 TRP cc_start: 0.6662 (m100) cc_final: 0.6297 (m100) REVERT: F 25 LYS cc_start: 0.8304 (ptmm) cc_final: 0.7972 (ptmt) REVERT: F 52 GLU cc_start: 0.7783 (pt0) cc_final: 0.7374 (tt0) REVERT: F 264 CYS cc_start: 0.8128 (m) cc_final: 0.7667 (m) REVERT: F 318 ASP cc_start: 0.6573 (p0) cc_final: 0.6067 (t0) REVERT: G 6 PRO cc_start: 0.8215 (Cg_endo) cc_final: 0.7813 (Cg_exo) REVERT: G 13 GLN cc_start: 0.7200 (tm-30) cc_final: 0.6507 (tm-30) REVERT: G 145 THR cc_start: 0.7673 (t) cc_final: 0.7365 (p) REVERT: G 184 GLU cc_start: 0.7235 (tt0) cc_final: 0.6879 (tp30) REVERT: H 1 MET cc_start: 0.4213 (mmt) cc_final: 0.3827 (mtt) REVERT: J 65 GLU cc_start: 0.4024 (tp30) cc_final: 0.3646 (tp30) REVERT: J 78 GLU cc_start: 0.6071 (tp30) cc_final: 0.5734 (mt-10) REVERT: J 102 GLU cc_start: 0.5842 (mm-30) cc_final: 0.4815 (tp30) REVERT: J 148 LEU cc_start: 0.6269 (mt) cc_final: 0.5950 (tt) REVERT: J 162 GLN cc_start: 0.6578 (pm20) cc_final: 0.5638 (pm20) REVERT: L 65 GLU cc_start: 0.5079 (pp20) cc_final: 0.3904 (tp30) REVERT: L 68 VAL cc_start: 0.4698 (t) cc_final: 0.4411 (m) REVERT: L 74 GLN cc_start: 0.6832 (mm-40) cc_final: 0.6534 (mm-40) REVERT: L 81 GLU cc_start: 0.7222 (pp20) cc_final: 0.5854 (mm-30) REVERT: L 141 GLU cc_start: 0.6139 (tt0) cc_final: 0.5510 (tp30) outliers start: 48 outliers final: 31 residues processed: 389 average time/residue: 0.4709 time to fit residues: 277.8001 Evaluate side-chains 328 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 295 time to evaluate : 3.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 274 ARG Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 161 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 281 optimal weight: 2.9990 chunk 230 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 339 optimal weight: 20.0000 chunk 366 optimal weight: 8.9990 chunk 302 optimal weight: 5.9990 chunk 336 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 272 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS C 571 GLN D 413 GLN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30110 Z= 0.188 Angle : 0.518 8.621 40807 Z= 0.262 Chirality : 0.043 0.156 4576 Planarity : 0.004 0.045 5333 Dihedral : 5.939 103.671 4231 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.07 % Allowed : 11.03 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.53 (0.14), residues: 3764 helix: 0.99 (0.13), residues: 1566 sheet: -0.45 (0.20), residues: 625 loop : 0.23 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 471 HIS 0.005 0.001 HIS E 375 PHE 0.011 0.001 PHE F 414 TYR 0.014 0.001 TYR D 463 ARG 0.007 0.000 ARG E 360 *********************** 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 368 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 335 time to evaluate : 3.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7504 (ttmt) cc_final: 0.7010 (tttt) REVERT: A 43 ASP cc_start: 0.6922 (t0) cc_final: 0.6452 (t0) REVERT: A 122 MET cc_start: 0.8160 (mtp) cc_final: 0.7687 (ttm) REVERT: A 124 LYS cc_start: 0.7441 (mtmm) cc_final: 0.7138 (mmtt) REVERT: A 180 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7688 (mt-10) REVERT: A 323 MET cc_start: 0.7981 (mpp) cc_final: 0.7715 (mmt) REVERT: A 408 ARG cc_start: 0.7484 (ttt180) cc_final: 0.7246 (ttm-80) REVERT: A 452 ASP cc_start: 0.6937 (m-30) cc_final: 0.6342 (m-30) REVERT: A 469 GLN cc_start: 0.6666 (OUTLIER) cc_final: 0.5385 (mp10) REVERT: B 33 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7462 (mm-30) REVERT: B 43 ASP cc_start: 0.7312 (t0) cc_final: 0.7072 (t70) REVERT: B 152 ASP cc_start: 0.6424 (p0) cc_final: 0.5980 (t70) REVERT: B 156 ARG cc_start: 0.7181 (ttm-80) cc_final: 0.6904 (mtm180) REVERT: B 197 ARG cc_start: 0.7413 (ttp-110) cc_final: 0.6993 (ttp-170) REVERT: B 271 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7570 (mt-10) REVERT: B 447 TYR cc_start: 0.6293 (t80) cc_final: 0.5955 (t80) REVERT: B 459 GLN cc_start: 0.6639 (tp-100) cc_final: 0.6408 (mm-40) REVERT: B 480 GLU cc_start: 0.6214 (mp0) cc_final: 0.5910 (mt-10) REVERT: B 493 ASP cc_start: 0.6093 (m-30) cc_final: 0.5664 (t0) REVERT: B 558 GLU cc_start: 0.6772 (mt-10) cc_final: 0.6511 (tp30) REVERT: C 124 LYS cc_start: 0.8281 (mppt) cc_final: 0.7745 (mmtt) REVERT: C 197 ARG cc_start: 0.7567 (ttp-110) cc_final: 0.7346 (mtm110) REVERT: C 343 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7378 (mt-10) REVERT: C 344 MET cc_start: 0.7814 (ttp) cc_final: 0.7388 (tpp) REVERT: C 374 GLU cc_start: 0.6579 (mt-10) cc_final: 0.6116 (mt-10) REVERT: C 408 ARG cc_start: 0.7034 (ttt180) cc_final: 0.6721 (ttt-90) REVERT: C 425 ASN cc_start: 0.7705 (m-40) cc_final: 0.7493 (m-40) REVERT: C 476 LEU cc_start: 0.5960 (OUTLIER) cc_final: 0.5534 (mt) REVERT: C 564 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7198 (tp30) REVERT: D 34 ASP cc_start: 0.7679 (m-30) cc_final: 0.7064 (p0) REVERT: D 74 SER cc_start: 0.8196 (p) cc_final: 0.7555 (t) REVERT: D 98 LYS cc_start: 0.7166 (mttt) cc_final: 0.6950 (mmtt) REVERT: D 259 ASP cc_start: 0.6905 (t70) cc_final: 0.6511 (t70) REVERT: D 264 CYS cc_start: 0.7741 (m) cc_final: 0.7035 (m) REVERT: D 368 LYS cc_start: 0.8113 (mtmt) cc_final: 0.7657 (mtmm) REVERT: D 377 GLN cc_start: 0.7045 (mt0) cc_final: 0.6779 (mm-40) REVERT: D 394 LYS cc_start: 0.7930 (ttmm) cc_final: 0.7658 (mtpt) REVERT: D 416 ASP cc_start: 0.7451 (t0) cc_final: 0.6826 (m-30) REVERT: D 428 GLN cc_start: 0.7545 (mt0) cc_final: 0.7169 (mt0) REVERT: E 15 SER cc_start: 0.8276 (t) cc_final: 0.7798 (p) REVERT: E 186 PRO cc_start: 0.7061 (Cg_exo) cc_final: 0.6716 (Cg_endo) REVERT: E 206 GLN cc_start: 0.7220 (tm-30) cc_final: 0.6977 (pt0) REVERT: E 250 ASP cc_start: 0.7720 (m-30) cc_final: 0.6706 (t0) REVERT: E 265 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: E 362 MET cc_start: 0.7821 (ttt) cc_final: 0.7506 (ttp) REVERT: E 421 PHE cc_start: 0.7226 (m-80) cc_final: 0.6473 (m-80) REVERT: E 440 TRP cc_start: 0.6618 (m100) cc_final: 0.6302 (m100) REVERT: F 25 LYS cc_start: 0.8298 (ptmm) cc_final: 0.8000 (ptmt) REVERT: F 264 CYS cc_start: 0.8121 (m) cc_final: 0.7662 (m) REVERT: F 318 ASP cc_start: 0.6444 (p0) cc_final: 0.5947 (t0) REVERT: F 450 GLU cc_start: 0.7048 (tp30) cc_final: 0.6755 (tp30) REVERT: G 6 PRO cc_start: 0.8146 (Cg_endo) cc_final: 0.7784 (Cg_exo) REVERT: G 13 GLN cc_start: 0.7139 (tm-30) cc_final: 0.6440 (tm-30) REVERT: G 145 THR cc_start: 0.7849 (t) cc_final: 0.7574 (p) REVERT: G 184 GLU cc_start: 0.7157 (tt0) cc_final: 0.6718 (tp30) REVERT: J 65 GLU cc_start: 0.4054 (tp30) cc_final: 0.3757 (tp30) REVERT: J 78 GLU cc_start: 0.6039 (tp30) cc_final: 0.5704 (mt-10) REVERT: J 102 GLU cc_start: 0.5813 (mm-30) cc_final: 0.4805 (tp30) REVERT: J 148 LEU cc_start: 0.6306 (mt) cc_final: 0.6031 (tt) REVERT: J 162 GLN cc_start: 0.6606 (pm20) cc_final: 0.6270 (pm20) REVERT: L 65 GLU cc_start: 0.5005 (pp20) cc_final: 0.3894 (tp30) REVERT: L 81 GLU cc_start: 0.7258 (pp20) cc_final: 0.5989 (mm-30) REVERT: L 82 GLU cc_start: 0.6040 (tp30) cc_final: 0.4816 (tt0) REVERT: L 141 GLU cc_start: 0.6075 (tt0) cc_final: 0.5480 (tp30) outliers start: 33 outliers final: 21 residues processed: 361 average time/residue: 0.4857 time to fit residues: 272.6192 Evaluate side-chains 335 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 311 time to evaluate : 3.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 274 ARG Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 5.9990 chunk 255 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 340 optimal weight: 20.0000 chunk 360 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 chunk 322 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 170 GLN F 437 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30110 Z= 0.176 Angle : 0.491 7.879 40807 Z= 0.247 Chirality : 0.043 0.167 4576 Planarity : 0.004 0.043 5333 Dihedral : 5.688 103.911 4231 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.49 % Allowed : 12.07 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 1.13 (0.14), residues: 1562 sheet: -0.45 (0.20), residues: 624 loop : 0.28 (0.17), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 119 HIS 0.004 0.001 HIS E 375 PHE 0.011 0.001 PHE B 559 TYR 0.013 0.001 TYR D 463 ARG 0.007 0.000 ARG B 488 *********************** 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 372 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 326 time to evaluate : 3.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7446 (ttmt) cc_final: 0.6947 (tttt) REVERT: A 122 MET cc_start: 0.8096 (mtp) cc_final: 0.7663 (ttm) REVERT: A 124 LYS cc_start: 0.7457 (mtmm) cc_final: 0.7165 (mmtt) REVERT: A 180 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7685 (mt-10) REVERT: A 323 MET cc_start: 0.7962 (mpp) cc_final: 0.7753 (mmt) REVERT: A 408 ARG cc_start: 0.7460 (ttt180) cc_final: 0.7216 (ttm-80) REVERT: A 452 ASP cc_start: 0.6923 (m-30) cc_final: 0.6325 (m-30) REVERT: A 469 GLN cc_start: 0.6625 (OUTLIER) cc_final: 0.6335 (mp10) REVERT: B 43 ASP cc_start: 0.7303 (t0) cc_final: 0.6916 (t70) REVERT: B 152 ASP cc_start: 0.6398 (p0) cc_final: 0.5929 (t70) REVERT: B 197 ARG cc_start: 0.7407 (ttp-110) cc_final: 0.6974 (ttp-170) REVERT: B 271 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7616 (mt-10) REVERT: B 447 TYR cc_start: 0.6290 (t80) cc_final: 0.5965 (t80) REVERT: B 459 GLN cc_start: 0.6653 (tp-100) cc_final: 0.6417 (mm-40) REVERT: B 480 GLU cc_start: 0.6308 (mp0) cc_final: 0.6003 (mt-10) REVERT: B 493 ASP cc_start: 0.6082 (m-30) cc_final: 0.5617 (t0) REVERT: B 558 GLU cc_start: 0.6757 (mt-10) cc_final: 0.6546 (tm-30) REVERT: C 124 LYS cc_start: 0.8174 (mppt) cc_final: 0.7629 (mmtt) REVERT: C 197 ARG cc_start: 0.7576 (ttp-110) cc_final: 0.7300 (mtm110) REVERT: C 343 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7361 (mt-10) REVERT: C 344 MET cc_start: 0.7876 (ttp) cc_final: 0.7438 (tpp) REVERT: C 374 GLU cc_start: 0.6602 (mt-10) cc_final: 0.6092 (mt-10) REVERT: C 408 ARG cc_start: 0.7062 (ttt180) cc_final: 0.6747 (ttt-90) REVERT: C 425 ASN cc_start: 0.7694 (m-40) cc_final: 0.7475 (m-40) REVERT: C 476 LEU cc_start: 0.6042 (OUTLIER) cc_final: 0.5567 (mt) REVERT: C 492 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6957 (tt0) REVERT: C 564 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7182 (tp30) REVERT: D 34 ASP cc_start: 0.7645 (m-30) cc_final: 0.7028 (p0) REVERT: D 74 SER cc_start: 0.8041 (p) cc_final: 0.7509 (t) REVERT: D 98 LYS cc_start: 0.7172 (mttt) cc_final: 0.6943 (mmtt) REVERT: D 209 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7450 (mm-30) REVERT: D 264 CYS cc_start: 0.7807 (m) cc_final: 0.7068 (m) REVERT: D 368 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7658 (mtmm) REVERT: D 377 GLN cc_start: 0.7011 (mt0) cc_final: 0.6723 (mm-40) REVERT: D 394 LYS cc_start: 0.7902 (ttmm) cc_final: 0.7625 (mtpt) REVERT: D 416 ASP cc_start: 0.7509 (t0) cc_final: 0.6846 (m-30) REVERT: E 186 PRO cc_start: 0.7061 (Cg_exo) cc_final: 0.6716 (Cg_endo) REVERT: E 206 GLN cc_start: 0.7186 (tm-30) cc_final: 0.6985 (pt0) REVERT: E 250 ASP cc_start: 0.7697 (m-30) cc_final: 0.6693 (t0) REVERT: E 265 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6703 (mp0) REVERT: E 362 MET cc_start: 0.7819 (ttt) cc_final: 0.7489 (ttp) REVERT: E 421 PHE cc_start: 0.7262 (m-80) cc_final: 0.6516 (m-80) REVERT: E 440 TRP cc_start: 0.6623 (m100) cc_final: 0.6336 (m100) REVERT: F 22 GLU cc_start: 0.7898 (pt0) cc_final: 0.7654 (pt0) REVERT: F 25 LYS cc_start: 0.8314 (ptmm) cc_final: 0.8015 (ptmt) REVERT: F 264 CYS cc_start: 0.8095 (m) cc_final: 0.7638 (m) REVERT: F 318 ASP cc_start: 0.6412 (p0) cc_final: 0.5951 (t0) REVERT: F 450 GLU cc_start: 0.7054 (tp30) cc_final: 0.6752 (tp30) REVERT: G 6 PRO cc_start: 0.8126 (Cg_endo) cc_final: 0.7762 (Cg_exo) REVERT: G 13 GLN cc_start: 0.7105 (tm-30) cc_final: 0.6775 (tm-30) REVERT: G 145 THR cc_start: 0.7842 (t) cc_final: 0.7571 (p) REVERT: G 184 GLU cc_start: 0.7158 (tt0) cc_final: 0.6728 (tp30) REVERT: J 65 GLU cc_start: 0.3952 (tp30) cc_final: 0.3665 (tp30) REVERT: J 78 GLU cc_start: 0.6065 (tp30) cc_final: 0.5737 (mt-10) REVERT: J 102 GLU cc_start: 0.5746 (mm-30) cc_final: 0.4775 (tp30) REVERT: J 148 LEU cc_start: 0.6332 (mt) cc_final: 0.6082 (tt) REVERT: L 65 GLU cc_start: 0.5030 (pp20) cc_final: 0.3893 (tp30) REVERT: L 67 LEU cc_start: 0.5802 (pp) cc_final: 0.5123 (tp) REVERT: L 68 VAL cc_start: 0.4960 (t) cc_final: 0.4744 (m) REVERT: L 81 GLU cc_start: 0.7181 (pp20) cc_final: 0.5936 (mm-30) REVERT: L 82 GLU cc_start: 0.6075 (tp30) cc_final: 0.4863 (tt0) REVERT: L 109 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6250 (mt) REVERT: L 141 GLU cc_start: 0.6034 (tt0) cc_final: 0.5456 (tp30) REVERT: L 145 GLU cc_start: 0.2608 (tp30) cc_final: 0.2184 (mm-30) outliers start: 46 outliers final: 31 residues processed: 364 average time/residue: 0.4387 time to fit residues: 249.0819 Evaluate side-chains 343 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 308 time to evaluate : 3.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 8.9990 chunk 204 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 268 optimal weight: 9.9990 chunk 148 optimal weight: 0.5980 chunk 307 optimal weight: 2.9990 chunk 249 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 323 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 206 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN J 162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 30110 Z= 0.418 Angle : 0.631 8.407 40807 Z= 0.318 Chirality : 0.048 0.190 4576 Planarity : 0.006 0.047 5333 Dihedral : 6.043 93.335 4231 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.34 % Allowed : 13.17 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.13 (0.14), residues: 3764 helix: 0.70 (0.13), residues: 1575 sheet: -0.65 (0.20), residues: 627 loop : -0.04 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 471 HIS 0.005 0.001 HIS B 185 PHE 0.017 0.002 PHE B 230 TYR 0.018 0.002 TYR B 562 ARG 0.006 0.001 ARG B 488 *********************** 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 370 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 298 time to evaluate : 3.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7642 (ttmt) cc_final: 0.7058 (tttt) REVERT: A 43 ASP cc_start: 0.7067 (t0) cc_final: 0.6752 (t0) REVERT: A 120 THR cc_start: 0.8377 (m) cc_final: 0.8016 (p) REVERT: A 122 MET cc_start: 0.8222 (mtp) cc_final: 0.7908 (ttm) REVERT: A 124 LYS cc_start: 0.7551 (mtmm) cc_final: 0.7218 (mmtt) REVERT: A 180 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7679 (mt-10) REVERT: A 323 MET cc_start: 0.7998 (mpp) cc_final: 0.7758 (mmt) REVERT: A 408 ARG cc_start: 0.7532 (ttt180) cc_final: 0.7229 (ttm-80) REVERT: A 452 ASP cc_start: 0.6942 (m-30) cc_final: 0.6348 (m-30) REVERT: A 469 GLN cc_start: 0.6700 (OUTLIER) cc_final: 0.5638 (mp10) REVERT: B 43 ASP cc_start: 0.7348 (t0) cc_final: 0.6830 (t0) REVERT: B 152 ASP cc_start: 0.6482 (p0) cc_final: 0.5998 (t70) REVERT: B 197 ARG cc_start: 0.7394 (ttp-110) cc_final: 0.6968 (ttp-170) REVERT: B 220 MET cc_start: 0.7156 (tpp) cc_final: 0.6947 (tpp) REVERT: B 271 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7717 (mt-10) REVERT: B 480 GLU cc_start: 0.6354 (mp0) cc_final: 0.6023 (mt-10) REVERT: B 493 ASP cc_start: 0.6161 (m-30) cc_final: 0.5754 (t0) REVERT: B 513 TYR cc_start: 0.5611 (t80) cc_final: 0.5274 (t80) REVERT: C 124 LYS cc_start: 0.8351 (mppt) cc_final: 0.7815 (mmtt) REVERT: C 197 ARG cc_start: 0.7536 (ttp-110) cc_final: 0.7262 (mtm110) REVERT: C 238 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.6692 (mt0) REVERT: C 274 ASP cc_start: 0.7728 (t0) cc_final: 0.7405 (t0) REVERT: C 343 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7394 (mt-10) REVERT: C 344 MET cc_start: 0.7864 (ttp) cc_final: 0.7502 (tpt) REVERT: C 374 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6192 (mt-10) REVERT: C 476 LEU cc_start: 0.6019 (OUTLIER) cc_final: 0.5619 (mt) REVERT: C 564 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7308 (tp30) REVERT: C 577 LEU cc_start: 0.2263 (OUTLIER) cc_final: 0.1568 (tp) REVERT: D 74 SER cc_start: 0.8306 (p) cc_final: 0.7943 (t) REVERT: D 98 LYS cc_start: 0.7207 (mttt) cc_final: 0.6949 (mmmt) REVERT: D 209 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7648 (mm-30) REVERT: D 259 ASP cc_start: 0.7275 (t70) cc_final: 0.6794 (t70) REVERT: D 264 CYS cc_start: 0.7755 (m) cc_final: 0.7052 (m) REVERT: D 368 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7676 (mtmm) REVERT: D 394 LYS cc_start: 0.8004 (ttmm) cc_final: 0.7712 (mtpt) REVERT: E 186 PRO cc_start: 0.7051 (Cg_exo) cc_final: 0.6636 (Cg_endo) REVERT: E 250 ASP cc_start: 0.7715 (m-30) cc_final: 0.6597 (t0) REVERT: E 265 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: E 362 MET cc_start: 0.7803 (ttt) cc_final: 0.7490 (ttp) REVERT: E 421 PHE cc_start: 0.7459 (m-80) cc_final: 0.6613 (m-80) REVERT: E 440 TRP cc_start: 0.6723 (m100) cc_final: 0.6462 (m100) REVERT: E 446 LEU cc_start: 0.6078 (mp) cc_final: 0.5265 (tp) REVERT: F 25 LYS cc_start: 0.8363 (ptmm) cc_final: 0.7948 (ptmt) REVERT: F 264 CYS cc_start: 0.8072 (m) cc_final: 0.7578 (m) REVERT: F 318 ASP cc_start: 0.6561 (OUTLIER) cc_final: 0.6229 (t0) REVERT: F 468 GLU cc_start: 0.6106 (mt-10) cc_final: 0.5802 (pp20) REVERT: G 6 PRO cc_start: 0.8177 (Cg_endo) cc_final: 0.7787 (Cg_exo) REVERT: G 13 GLN cc_start: 0.7173 (tm-30) cc_final: 0.6528 (tm-30) REVERT: G 38 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6957 (tt0) REVERT: G 145 THR cc_start: 0.7742 (t) cc_final: 0.7435 (p) REVERT: G 166 GLN cc_start: 0.7251 (mm-40) cc_final: 0.6511 (tt0) REVERT: G 184 GLU cc_start: 0.7275 (tt0) cc_final: 0.6812 (tp30) REVERT: J 78 GLU cc_start: 0.6131 (tp30) cc_final: 0.5797 (mt-10) REVERT: J 102 GLU cc_start: 0.5754 (mm-30) cc_final: 0.4852 (tp30) REVERT: L 65 GLU cc_start: 0.5131 (pp20) cc_final: 0.3857 (tp30) REVERT: L 68 VAL cc_start: 0.4962 (t) cc_final: 0.4741 (m) REVERT: L 81 GLU cc_start: 0.7150 (pp20) cc_final: 0.5939 (mm-30) REVERT: L 141 GLU cc_start: 0.6161 (tt0) cc_final: 0.5359 (tp30) outliers start: 72 outliers final: 50 residues processed: 362 average time/residue: 0.4366 time to fit residues: 251.5003 Evaluate side-chains 339 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 282 time to evaluate : 3.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 238 GLN Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 162 GLN Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 0.9980 chunk 324 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 211 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 360 optimal weight: 9.9990 chunk 299 optimal weight: 0.4980 chunk 167 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 377 GLN ** F 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30110 Z= 0.154 Angle : 0.489 8.255 40807 Z= 0.247 Chirality : 0.042 0.177 4576 Planarity : 0.004 0.047 5333 Dihedral : 5.677 100.245 4231 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.69 % Allowed : 14.53 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.47 (0.14), residues: 3764 helix: 1.01 (0.14), residues: 1570 sheet: -0.58 (0.20), residues: 615 loop : 0.17 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 424 HIS 0.004 0.001 HIS E 375 PHE 0.010 0.001 PHE F 418 TYR 0.013 0.001 TYR D 463 ARG 0.009 0.000 ARG B 488 *********************** 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 360 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 308 time to evaluate : 3.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7491 (ttmt) cc_final: 0.6970 (tttt) REVERT: A 120 THR cc_start: 0.8322 (m) cc_final: 0.7947 (p) REVERT: A 122 MET cc_start: 0.8142 (mtp) cc_final: 0.7786 (ttm) REVERT: A 124 LYS cc_start: 0.7525 (mtmm) cc_final: 0.7212 (mmtt) REVERT: A 180 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7697 (mt-10) REVERT: A 408 ARG cc_start: 0.7518 (ttt180) cc_final: 0.7206 (ttm-80) REVERT: A 452 ASP cc_start: 0.6916 (m-30) cc_final: 0.6305 (m-30) REVERT: A 469 GLN cc_start: 0.6615 (OUTLIER) cc_final: 0.5374 (mp10) REVERT: B 43 ASP cc_start: 0.7268 (t0) cc_final: 0.6947 (t70) REVERT: B 152 ASP cc_start: 0.6431 (p0) cc_final: 0.5940 (t70) REVERT: B 197 ARG cc_start: 0.7399 (ttp-110) cc_final: 0.6980 (ttp-170) REVERT: B 271 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7687 (mt-10) REVERT: B 390 ASP cc_start: 0.6941 (t0) cc_final: 0.6600 (p0) REVERT: B 480 GLU cc_start: 0.6317 (mp0) cc_final: 0.5987 (mt-10) REVERT: B 488 ARG cc_start: 0.6675 (ttp80) cc_final: 0.5479 (mtp180) REVERT: B 493 ASP cc_start: 0.6078 (m-30) cc_final: 0.5747 (t0) REVERT: B 520 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.6240 (tt) REVERT: C 124 LYS cc_start: 0.8263 (mppt) cc_final: 0.7723 (mmtt) REVERT: C 274 ASP cc_start: 0.7787 (t0) cc_final: 0.7562 (t0) REVERT: C 343 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7347 (mt-10) REVERT: C 344 MET cc_start: 0.7859 (ttp) cc_final: 0.7435 (tpp) REVERT: C 374 GLU cc_start: 0.6607 (mt-10) cc_final: 0.6081 (mt-10) REVERT: C 476 LEU cc_start: 0.6065 (OUTLIER) cc_final: 0.5651 (mt) REVERT: C 492 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6932 (tt0) REVERT: C 564 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7203 (tp30) REVERT: D 6 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7426 (mmmt) REVERT: D 98 LYS cc_start: 0.7117 (mttt) cc_final: 0.6890 (mmtt) REVERT: D 209 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7522 (mm-30) REVERT: D 264 CYS cc_start: 0.7792 (m) cc_final: 0.7029 (m) REVERT: D 268 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.6759 (ttt180) REVERT: D 368 LYS cc_start: 0.8132 (mtmt) cc_final: 0.7670 (mtmm) REVERT: D 394 LYS cc_start: 0.7879 (ttmm) cc_final: 0.7616 (mtpt) REVERT: D 416 ASP cc_start: 0.7464 (t70) cc_final: 0.6876 (m-30) REVERT: E 186 PRO cc_start: 0.7135 (Cg_exo) cc_final: 0.6785 (Cg_endo) REVERT: E 209 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7644 (mm-30) REVERT: E 250 ASP cc_start: 0.7676 (m-30) cc_final: 0.6668 (t0) REVERT: E 265 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: E 362 MET cc_start: 0.7802 (ttt) cc_final: 0.7482 (ttp) REVERT: E 421 PHE cc_start: 0.7417 (m-80) cc_final: 0.6578 (m-80) REVERT: E 440 TRP cc_start: 0.6706 (m100) cc_final: 0.6480 (m100) REVERT: E 446 LEU cc_start: 0.6014 (mp) cc_final: 0.5358 (tp) REVERT: F 22 GLU cc_start: 0.7874 (pt0) cc_final: 0.7608 (pt0) REVERT: F 25 LYS cc_start: 0.8312 (ptmm) cc_final: 0.7935 (ptmt) REVERT: F 34 ASP cc_start: 0.6858 (m-30) cc_final: 0.6651 (m-30) REVERT: F 264 CYS cc_start: 0.8129 (m) cc_final: 0.7696 (m) REVERT: F 318 ASP cc_start: 0.6370 (OUTLIER) cc_final: 0.6022 (t0) REVERT: F 420 ARG cc_start: 0.7229 (mtp-110) cc_final: 0.6730 (ttm-80) REVERT: G 6 PRO cc_start: 0.8142 (Cg_endo) cc_final: 0.7762 (Cg_exo) REVERT: G 13 GLN cc_start: 0.7156 (tm-30) cc_final: 0.6498 (tm-30) REVERT: G 38 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7002 (tt0) REVERT: G 145 THR cc_start: 0.7838 (t) cc_final: 0.7553 (p) REVERT: G 166 GLN cc_start: 0.7130 (mm-40) cc_final: 0.6434 (tt0) REVERT: G 184 GLU cc_start: 0.7192 (tt0) cc_final: 0.6785 (tp30) REVERT: J 78 GLU cc_start: 0.6146 (tp30) cc_final: 0.5721 (mt-10) REVERT: J 102 GLU cc_start: 0.5655 (mm-30) cc_final: 0.4816 (tp30) REVERT: J 148 LEU cc_start: 0.5004 (OUTLIER) cc_final: 0.4614 (pp) REVERT: L 65 GLU cc_start: 0.5122 (pp20) cc_final: 0.3887 (mt-10) REVERT: L 81 GLU cc_start: 0.7142 (pp20) cc_final: 0.5993 (mm-30) REVERT: L 82 GLU cc_start: 0.6070 (tp30) cc_final: 0.4818 (tt0) REVERT: L 109 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6374 (mt) REVERT: L 141 GLU cc_start: 0.6118 (tt0) cc_final: 0.5430 (tp30) outliers start: 52 outliers final: 27 residues processed: 354 average time/residue: 0.4483 time to fit residues: 249.6391 Evaluate side-chains 330 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 293 time to evaluate : 3.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 263 optimal weight: 5.9990 chunk 204 optimal weight: 0.9980 chunk 303 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 359 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS E 129 GLN F 23 ASN F 206 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN J 162 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 30110 Z= 0.370 Angle : 0.587 7.648 40807 Z= 0.296 Chirality : 0.046 0.195 4576 Planarity : 0.005 0.049 5333 Dihedral : 5.863 93.489 4231 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.47 % Allowed : 14.56 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.20 (0.14), residues: 3764 helix: 0.80 (0.13), residues: 1571 sheet: -0.65 (0.20), residues: 615 loop : -0.04 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 424 HIS 0.004 0.001 HIS E 375 PHE 0.026 0.002 PHE G 108 TYR 0.016 0.002 TYR G 133 ARG 0.005 0.001 ARG C 130 *********************** 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 369 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 293 time to evaluate : 3.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7634 (ttmt) cc_final: 0.7057 (tttt) REVERT: A 43 ASP cc_start: 0.7118 (t0) cc_final: 0.6837 (t0) REVERT: A 120 THR cc_start: 0.8381 (m) cc_final: 0.8005 (p) REVERT: A 122 MET cc_start: 0.8204 (mtp) cc_final: 0.7954 (ttm) REVERT: A 124 LYS cc_start: 0.7468 (mtmm) cc_final: 0.7137 (mmtt) REVERT: A 180 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7703 (mt-10) REVERT: A 452 ASP cc_start: 0.6945 (m-30) cc_final: 0.6343 (m-30) REVERT: A 469 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.5523 (mp10) REVERT: B 43 ASP cc_start: 0.7363 (t0) cc_final: 0.6858 (t0) REVERT: B 152 ASP cc_start: 0.6485 (p0) cc_final: 0.5993 (t70) REVERT: B 197 ARG cc_start: 0.7374 (ttp-110) cc_final: 0.6957 (ttp-170) REVERT: B 271 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7801 (mt-10) REVERT: B 390 ASP cc_start: 0.6977 (t0) cc_final: 0.6672 (p0) REVERT: B 480 GLU cc_start: 0.6360 (mp0) cc_final: 0.6032 (mt-10) REVERT: B 493 ASP cc_start: 0.6024 (m-30) cc_final: 0.5799 (t0) REVERT: B 520 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.6171 (tt) REVERT: C 124 LYS cc_start: 0.8397 (mppt) cc_final: 0.7885 (mmtt) REVERT: C 238 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7106 (mt0) REVERT: C 274 ASP cc_start: 0.7784 (t0) cc_final: 0.7428 (t0) REVERT: C 343 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7394 (mt-10) REVERT: C 344 MET cc_start: 0.7877 (ttp) cc_final: 0.7518 (tpt) REVERT: C 374 GLU cc_start: 0.6627 (mt-10) cc_final: 0.6153 (mt-10) REVERT: C 476 LEU cc_start: 0.6047 (OUTLIER) cc_final: 0.5664 (mt) REVERT: C 492 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6893 (tt0) REVERT: C 564 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7256 (tp30) REVERT: C 577 LEU cc_start: 0.2015 (OUTLIER) cc_final: 0.1060 (tp) REVERT: D 98 LYS cc_start: 0.7146 (mttt) cc_final: 0.6901 (mmmt) REVERT: D 209 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7639 (mm-30) REVERT: D 264 CYS cc_start: 0.7803 (m) cc_final: 0.7056 (m) REVERT: D 268 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.6828 (ttt180) REVERT: D 368 LYS cc_start: 0.8141 (mtmt) cc_final: 0.7682 (mtmm) REVERT: D 394 LYS cc_start: 0.7970 (ttmm) cc_final: 0.7679 (mtpt) REVERT: E 4 LEU cc_start: 0.0851 (OUTLIER) cc_final: 0.0309 (tp) REVERT: E 130 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.7525 (p90) REVERT: E 186 PRO cc_start: 0.7092 (Cg_exo) cc_final: 0.6690 (Cg_endo) REVERT: E 250 ASP cc_start: 0.7724 (m-30) cc_final: 0.6602 (t0) REVERT: E 265 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6666 (mp0) REVERT: E 362 MET cc_start: 0.7804 (ttt) cc_final: 0.7504 (ttp) REVERT: E 421 PHE cc_start: 0.7440 (m-80) cc_final: 0.6576 (m-80) REVERT: E 440 TRP cc_start: 0.6699 (m100) cc_final: 0.6474 (m100) REVERT: E 446 LEU cc_start: 0.6029 (mp) cc_final: 0.5265 (tp) REVERT: F 25 LYS cc_start: 0.8333 (ptmm) cc_final: 0.7934 (ptmt) REVERT: F 264 CYS cc_start: 0.8060 (m) cc_final: 0.7591 (m) REVERT: F 318 ASP cc_start: 0.6495 (OUTLIER) cc_final: 0.6201 (t0) REVERT: F 450 GLU cc_start: 0.7177 (tp30) cc_final: 0.6934 (tp30) REVERT: F 468 GLU cc_start: 0.6146 (mt-10) cc_final: 0.5832 (pp20) REVERT: G 6 PRO cc_start: 0.8178 (Cg_endo) cc_final: 0.7782 (Cg_exo) REVERT: G 13 GLN cc_start: 0.7163 (tm-30) cc_final: 0.6520 (tm-30) REVERT: G 38 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6963 (tt0) REVERT: G 145 THR cc_start: 0.7755 (t) cc_final: 0.7442 (p) REVERT: G 166 GLN cc_start: 0.7252 (mm-40) cc_final: 0.6534 (tt0) REVERT: G 184 GLU cc_start: 0.7308 (tt0) cc_final: 0.6820 (tp30) REVERT: J 78 GLU cc_start: 0.6199 (tp30) cc_final: 0.5769 (mt-10) REVERT: J 102 GLU cc_start: 0.5642 (mm-30) cc_final: 0.4858 (tp30) REVERT: J 127 ASP cc_start: 0.5207 (OUTLIER) cc_final: 0.4516 (t0) REVERT: L 81 GLU cc_start: 0.7184 (pp20) cc_final: 0.6072 (mm-30) REVERT: L 109 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6535 (mt) REVERT: L 141 GLU cc_start: 0.6231 (tt0) cc_final: 0.5455 (tp30) outliers start: 76 outliers final: 44 residues processed: 358 average time/residue: 0.4446 time to fit residues: 248.7672 Evaluate side-chains 343 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 286 time to evaluate : 3.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 238 GLN Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 182 VAL 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: 5.9990 chunk 214 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 228 optimal weight: 0.2980 chunk 244 optimal weight: 4.9990 chunk 177 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 282 optimal weight: 5.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN F 437 GLN J 162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 30110 Z= 0.300 Angle : 0.546 7.996 40807 Z= 0.276 Chirality : 0.044 0.191 4576 Planarity : 0.005 0.050 5333 Dihedral : 5.759 94.137 4231 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.21 % Allowed : 14.89 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.20 (0.14), residues: 3764 helix: 0.79 (0.13), residues: 1571 sheet: -0.65 (0.21), residues: 615 loop : -0.04 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 424 HIS 0.004 0.001 HIS E 375 PHE 0.018 0.002 PHE G 108 TYR 0.019 0.001 TYR B 513 ARG 0.009 0.000 ARG B 488 *********************** 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 355 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 287 time to evaluate : 3.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7596 (ttmt) cc_final: 0.7099 (tttt) REVERT: A 43 ASP cc_start: 0.7096 (t0) cc_final: 0.6835 (t0) REVERT: A 120 THR cc_start: 0.8387 (m) cc_final: 0.8006 (p) REVERT: A 122 MET cc_start: 0.8174 (mtp) cc_final: 0.7898 (ttm) REVERT: A 124 LYS cc_start: 0.7514 (mtmm) cc_final: 0.7171 (mmtt) REVERT: A 180 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7677 (mt-10) REVERT: A 452 ASP cc_start: 0.6936 (m-30) cc_final: 0.6345 (m-30) REVERT: A 469 GLN cc_start: 0.6663 (OUTLIER) cc_final: 0.5476 (mp10) REVERT: B 43 ASP cc_start: 0.7349 (t0) cc_final: 0.7022 (t70) REVERT: B 152 ASP cc_start: 0.6481 (p0) cc_final: 0.5987 (t70) REVERT: B 197 ARG cc_start: 0.7319 (ttp-110) cc_final: 0.6902 (ttp-170) REVERT: B 271 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7807 (mt-10) REVERT: B 390 ASP cc_start: 0.7007 (t0) cc_final: 0.6710 (p0) REVERT: B 480 GLU cc_start: 0.6400 (mp0) cc_final: 0.6072 (mt-10) REVERT: B 488 ARG cc_start: 0.6637 (ttp80) cc_final: 0.5436 (mtp180) REVERT: B 520 LEU cc_start: 0.6379 (OUTLIER) cc_final: 0.6126 (tt) REVERT: C 124 LYS cc_start: 0.8369 (mppt) cc_final: 0.7885 (mmtt) REVERT: C 274 ASP cc_start: 0.7757 (t0) cc_final: 0.7438 (t0) REVERT: C 344 MET cc_start: 0.7922 (ttp) cc_final: 0.7449 (tpt) REVERT: C 348 GLU cc_start: 0.7695 (mp0) cc_final: 0.7335 (mp0) REVERT: C 374 GLU cc_start: 0.6603 (mt-10) cc_final: 0.6130 (mt-10) REVERT: C 476 LEU cc_start: 0.6027 (OUTLIER) cc_final: 0.5654 (mt) REVERT: C 492 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6930 (tt0) REVERT: D 9 THR cc_start: 0.7225 (OUTLIER) cc_final: 0.6449 (p) REVERT: D 98 LYS cc_start: 0.7109 (mttt) cc_final: 0.6877 (mmmt) REVERT: D 209 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7596 (mm-30) REVERT: D 264 CYS cc_start: 0.7801 (m) cc_final: 0.7047 (m) REVERT: D 268 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.6859 (ttt180) REVERT: D 290 ASP cc_start: 0.6934 (OUTLIER) cc_final: 0.6350 (t70) REVERT: D 368 LYS cc_start: 0.8142 (mtmt) cc_final: 0.7702 (mtmm) REVERT: D 394 LYS cc_start: 0.7936 (ttmm) cc_final: 0.7651 (mtpt) REVERT: D 416 ASP cc_start: 0.7547 (t70) cc_final: 0.6885 (m-30) REVERT: E 4 LEU cc_start: 0.1013 (OUTLIER) cc_final: 0.0425 (tp) REVERT: E 130 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7457 (p90) REVERT: E 186 PRO cc_start: 0.7106 (Cg_exo) cc_final: 0.6724 (Cg_endo) REVERT: E 250 ASP cc_start: 0.7722 (m-30) cc_final: 0.6615 (t0) REVERT: E 265 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: E 362 MET cc_start: 0.7806 (ttt) cc_final: 0.7501 (ttp) REVERT: E 421 PHE cc_start: 0.7452 (m-80) cc_final: 0.6606 (m-80) REVERT: E 440 TRP cc_start: 0.6654 (m100) cc_final: 0.6430 (m100) REVERT: E 446 LEU cc_start: 0.5933 (mp) cc_final: 0.5267 (tp) REVERT: F 22 GLU cc_start: 0.7893 (pt0) cc_final: 0.7618 (pt0) REVERT: F 25 LYS cc_start: 0.8062 (ptmm) cc_final: 0.7727 (ptmt) REVERT: F 53 GLU cc_start: 0.7120 (tt0) cc_final: 0.6796 (pt0) REVERT: F 264 CYS cc_start: 0.8114 (m) cc_final: 0.7661 (m) REVERT: F 318 ASP cc_start: 0.6374 (OUTLIER) cc_final: 0.6079 (t0) REVERT: F 420 ARG cc_start: 0.7332 (mtp-110) cc_final: 0.6780 (ttm-80) REVERT: F 450 GLU cc_start: 0.7210 (tp30) cc_final: 0.6923 (tp30) REVERT: G 6 PRO cc_start: 0.8123 (Cg_endo) cc_final: 0.7713 (Cg_exo) REVERT: G 13 GLN cc_start: 0.7171 (tm-30) cc_final: 0.6494 (tm-30) REVERT: G 38 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6895 (tt0) REVERT: G 145 THR cc_start: 0.7743 (t) cc_final: 0.7421 (p) REVERT: G 166 GLN cc_start: 0.7268 (mm-40) cc_final: 0.6611 (tt0) REVERT: G 184 GLU cc_start: 0.7295 (tt0) cc_final: 0.6815 (tp30) REVERT: J 78 GLU cc_start: 0.6164 (tp30) cc_final: 0.5793 (mt-10) REVERT: J 102 GLU cc_start: 0.5514 (mm-30) cc_final: 0.4762 (tp30) REVERT: L 65 GLU cc_start: 0.5267 (pp20) cc_final: 0.3729 (tp30) REVERT: L 81 GLU cc_start: 0.7159 (pp20) cc_final: 0.6156 (mm-30) REVERT: L 109 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6616 (mt) REVERT: L 141 GLU cc_start: 0.6160 (tt0) cc_final: 0.5399 (tp30) outliers start: 68 outliers final: 47 residues processed: 344 average time/residue: 0.4228 time to fit residues: 229.6259 Evaluate side-chains 338 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 279 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 568 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 2.9990 chunk 344 optimal weight: 4.9990 chunk 314 optimal weight: 6.9990 chunk 335 optimal weight: 30.0000 chunk 201 optimal weight: 0.6980 chunk 145 optimal weight: 0.7980 chunk 263 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 302 optimal weight: 8.9990 chunk 316 optimal weight: 20.0000 chunk 333 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN F 206 GLN F 437 GLN J 162 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30110 Z= 0.260 Angle : 0.529 7.660 40807 Z= 0.267 Chirality : 0.044 0.197 4576 Planarity : 0.004 0.050 5333 Dihedral : 5.639 95.338 4231 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.27 % Allowed : 14.99 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.26 (0.14), residues: 3764 helix: 0.85 (0.13), residues: 1571 sheet: -0.65 (0.21), residues: 615 loop : 0.00 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 424 HIS 0.004 0.001 HIS E 375 PHE 0.016 0.001 PHE G 108 TYR 0.013 0.001 TYR D 463 ARG 0.008 0.000 ARG B 488 *********************** 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 352 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 282 time to evaluate : 3.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7599 (ttmt) cc_final: 0.7107 (tttt) REVERT: A 43 ASP cc_start: 0.7055 (t0) cc_final: 0.6806 (t0) REVERT: A 120 THR cc_start: 0.8354 (m) cc_final: 0.7960 (p) REVERT: A 122 MET cc_start: 0.8140 (mtp) cc_final: 0.7855 (ttm) REVERT: A 124 LYS cc_start: 0.7466 (mtmm) cc_final: 0.7143 (mmtt) REVERT: A 180 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7675 (mt-10) REVERT: A 452 ASP cc_start: 0.6941 (m-30) cc_final: 0.6346 (m-30) REVERT: A 469 GLN cc_start: 0.6674 (OUTLIER) cc_final: 0.5445 (mp10) REVERT: B 43 ASP cc_start: 0.7314 (t0) cc_final: 0.7004 (t70) REVERT: B 152 ASP cc_start: 0.6468 (p0) cc_final: 0.5963 (t70) REVERT: B 197 ARG cc_start: 0.7330 (ttp-110) cc_final: 0.7021 (ttp-170) REVERT: B 271 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7843 (mt-10) REVERT: B 390 ASP cc_start: 0.7010 (t0) cc_final: 0.6747 (p0) REVERT: B 480 GLU cc_start: 0.6396 (mp0) cc_final: 0.6064 (mt-10) REVERT: B 488 ARG cc_start: 0.6498 (ttp80) cc_final: 0.5404 (mtp180) REVERT: B 520 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.6152 (tt) REVERT: C 124 LYS cc_start: 0.8379 (mppt) cc_final: 0.7780 (mmtt) REVERT: C 133 MET cc_start: 0.6534 (mtt) cc_final: 0.6282 (mtt) REVERT: C 274 ASP cc_start: 0.7795 (t0) cc_final: 0.7437 (t0) REVERT: C 344 MET cc_start: 0.7997 (ttp) cc_final: 0.7476 (tpp) REVERT: C 374 GLU cc_start: 0.6586 (mt-10) cc_final: 0.6134 (mt-10) REVERT: C 476 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5653 (mt) REVERT: C 492 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6941 (tt0) REVERT: C 577 LEU cc_start: 0.1899 (OUTLIER) cc_final: 0.0968 (tp) REVERT: D 9 THR cc_start: 0.7255 (OUTLIER) cc_final: 0.6498 (p) REVERT: D 98 LYS cc_start: 0.7107 (mttt) cc_final: 0.6878 (mmmt) REVERT: D 209 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7592 (mm-30) REVERT: D 264 CYS cc_start: 0.7807 (m) cc_final: 0.7060 (m) REVERT: D 268 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.6832 (ttt180) REVERT: D 290 ASP cc_start: 0.6911 (OUTLIER) cc_final: 0.6308 (t70) REVERT: D 368 LYS cc_start: 0.8146 (mtmt) cc_final: 0.7705 (mtmm) REVERT: D 394 LYS cc_start: 0.7925 (ttmm) cc_final: 0.7643 (mtpt) REVERT: D 416 ASP cc_start: 0.7553 (t70) cc_final: 0.6903 (m-30) REVERT: E 4 LEU cc_start: 0.1025 (OUTLIER) cc_final: 0.0462 (tp) REVERT: E 130 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7466 (p90) REVERT: E 186 PRO cc_start: 0.7157 (Cg_exo) cc_final: 0.6796 (Cg_endo) REVERT: E 250 ASP cc_start: 0.7709 (m-30) cc_final: 0.6640 (t0) REVERT: E 265 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6690 (mp0) REVERT: E 362 MET cc_start: 0.7801 (ttt) cc_final: 0.7500 (ttp) REVERT: E 421 PHE cc_start: 0.7433 (m-80) cc_final: 0.6598 (m-80) REVERT: E 440 TRP cc_start: 0.6541 (m100) cc_final: 0.6322 (m100) REVERT: E 446 LEU cc_start: 0.5850 (mp) cc_final: 0.5213 (tp) REVERT: F 22 GLU cc_start: 0.7851 (pt0) cc_final: 0.7635 (pt0) REVERT: F 25 LYS cc_start: 0.8058 (ptmm) cc_final: 0.7744 (ptmt) REVERT: F 53 GLU cc_start: 0.7055 (tt0) cc_final: 0.6760 (pt0) REVERT: F 264 CYS cc_start: 0.8102 (m) cc_final: 0.7653 (m) REVERT: F 318 ASP cc_start: 0.6402 (OUTLIER) cc_final: 0.6110 (t0) REVERT: F 420 ARG cc_start: 0.7321 (mtp-110) cc_final: 0.6790 (ttm-80) REVERT: F 450 GLU cc_start: 0.7222 (tp30) cc_final: 0.6914 (tp30) REVERT: G 6 PRO cc_start: 0.8169 (Cg_endo) cc_final: 0.7754 (Cg_exo) REVERT: G 13 GLN cc_start: 0.7147 (tm-30) cc_final: 0.6489 (tm-30) REVERT: G 38 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6895 (tt0) REVERT: G 145 THR cc_start: 0.7751 (t) cc_final: 0.7434 (p) REVERT: G 166 GLN cc_start: 0.7279 (mm-40) cc_final: 0.6613 (tt0) REVERT: G 184 GLU cc_start: 0.7298 (tt0) cc_final: 0.6835 (tp30) REVERT: J 78 GLU cc_start: 0.6117 (tp30) cc_final: 0.5756 (mt-10) REVERT: J 102 GLU cc_start: 0.5528 (mm-30) cc_final: 0.4767 (tp30) REVERT: J 127 ASP cc_start: 0.5205 (OUTLIER) cc_final: 0.4520 (t0) REVERT: L 65 GLU cc_start: 0.5352 (pp20) cc_final: 0.3732 (tp30) REVERT: L 81 GLU cc_start: 0.7130 (pp20) cc_final: 0.6158 (mm-30) REVERT: L 82 GLU cc_start: 0.6192 (tp30) cc_final: 0.4830 (tt0) REVERT: L 109 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6635 (mt) REVERT: L 141 GLU cc_start: 0.6156 (tt0) cc_final: 0.5385 (tp30) outliers start: 70 outliers final: 48 residues processed: 342 average time/residue: 0.4374 time to fit residues: 234.8720 Evaluate side-chains 339 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 277 time to evaluate : 3.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 568 LYS Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 4.9990 chunk 354 optimal weight: 7.9990 chunk 216 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 246 optimal weight: 1.9990 chunk 371 optimal weight: 1.9990 chunk 342 optimal weight: 5.9990 chunk 295 optimal weight: 0.9980 chunk 30 optimal weight: 0.0270 chunk 228 optimal weight: 4.9990 chunk 181 optimal weight: 0.5980 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN D 381 GLN E 465 GLN ** F 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30110 Z= 0.162 Angle : 0.485 7.460 40807 Z= 0.246 Chirality : 0.042 0.201 4576 Planarity : 0.004 0.049 5333 Dihedral : 5.402 100.244 4231 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.78 % Allowed : 15.50 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.52 (0.14), residues: 3764 helix: 1.04 (0.14), residues: 1561 sheet: -0.55 (0.21), residues: 614 loop : 0.20 (0.17), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 424 HIS 0.004 0.001 HIS E 375 PHE 0.014 0.001 PHE G 108 TYR 0.013 0.001 TYR F 54 ARG 0.008 0.000 ARG B 488 ********************** 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 344 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 289 time to evaluate : 3.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7512 (ttmt) cc_final: 0.7048 (tttt) REVERT: A 120 THR cc_start: 0.8322 (m) cc_final: 0.7933 (p) REVERT: A 122 MET cc_start: 0.8136 (mtp) cc_final: 0.7832 (ttm) REVERT: A 124 LYS cc_start: 0.7462 (mtmm) cc_final: 0.7151 (mmtt) REVERT: A 180 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7665 (mt-10) REVERT: A 452 ASP cc_start: 0.6928 (m-30) cc_final: 0.6321 (m-30) REVERT: A 469 GLN cc_start: 0.6620 (OUTLIER) cc_final: 0.5429 (mp10) REVERT: B 43 ASP cc_start: 0.7281 (t0) cc_final: 0.6945 (t70) REVERT: B 152 ASP cc_start: 0.6432 (p0) cc_final: 0.5913 (t70) REVERT: B 197 ARG cc_start: 0.7385 (ttp-110) cc_final: 0.7077 (ttp-170) REVERT: B 271 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7792 (mt-10) REVERT: B 480 GLU cc_start: 0.6407 (mp0) cc_final: 0.6075 (mt-10) REVERT: B 488 ARG cc_start: 0.6489 (ttp80) cc_final: 0.5350 (mtp180) REVERT: B 520 LEU cc_start: 0.6375 (OUTLIER) cc_final: 0.6147 (tt) REVERT: C 124 LYS cc_start: 0.8344 (mppt) cc_final: 0.7722 (mmtt) REVERT: C 133 MET cc_start: 0.6495 (mtt) cc_final: 0.6231 (mtt) REVERT: C 274 ASP cc_start: 0.7789 (t0) cc_final: 0.7456 (t0) REVERT: C 343 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7330 (mt-10) REVERT: C 344 MET cc_start: 0.7905 (ttp) cc_final: 0.7485 (tpp) REVERT: C 348 GLU cc_start: 0.7641 (mp0) cc_final: 0.7340 (mp0) REVERT: C 476 LEU cc_start: 0.6106 (OUTLIER) cc_final: 0.5656 (mt) REVERT: C 492 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6938 (tt0) REVERT: D 9 THR cc_start: 0.7300 (OUTLIER) cc_final: 0.6556 (p) REVERT: D 98 LYS cc_start: 0.7168 (mttt) cc_final: 0.6933 (mmmt) REVERT: D 209 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7528 (mm-30) REVERT: D 264 CYS cc_start: 0.7789 (m) cc_final: 0.7016 (m) REVERT: D 268 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.6767 (ttt180) REVERT: D 290 ASP cc_start: 0.6848 (OUTLIER) cc_final: 0.6219 (t70) REVERT: D 368 LYS cc_start: 0.8167 (mtmt) cc_final: 0.7671 (mtmm) REVERT: D 394 LYS cc_start: 0.7862 (ttmm) cc_final: 0.7592 (mtpt) REVERT: D 416 ASP cc_start: 0.7500 (t70) cc_final: 0.6890 (m-30) REVERT: E 4 LEU cc_start: 0.1070 (OUTLIER) cc_final: 0.0505 (tp) REVERT: E 130 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7431 (p90) REVERT: E 186 PRO cc_start: 0.7178 (Cg_exo) cc_final: 0.6834 (Cg_endo) REVERT: E 209 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7570 (tm-30) REVERT: E 250 ASP cc_start: 0.7700 (m-30) cc_final: 0.6662 (t0) REVERT: E 265 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6765 (mp0) REVERT: E 353 ASP cc_start: 0.7368 (t70) cc_final: 0.7051 (p0) REVERT: E 362 MET cc_start: 0.7820 (ttt) cc_final: 0.7517 (ttp) REVERT: E 421 PHE cc_start: 0.7395 (m-80) cc_final: 0.6595 (m-80) REVERT: E 446 LEU cc_start: 0.6097 (mp) cc_final: 0.5545 (tp) REVERT: F 22 GLU cc_start: 0.7771 (pt0) cc_final: 0.7545 (pt0) REVERT: F 25 LYS cc_start: 0.8054 (ptmm) cc_final: 0.7755 (ptmt) REVERT: F 53 GLU cc_start: 0.7081 (tt0) cc_final: 0.6760 (pt0) REVERT: F 264 CYS cc_start: 0.8068 (m) cc_final: 0.7618 (m) REVERT: F 318 ASP cc_start: 0.6317 (OUTLIER) cc_final: 0.5998 (t0) REVERT: F 420 ARG cc_start: 0.7346 (mtp-110) cc_final: 0.6829 (ttm-80) REVERT: F 450 GLU cc_start: 0.7223 (tp30) cc_final: 0.6901 (tp30) REVERT: G 6 PRO cc_start: 0.8093 (Cg_endo) cc_final: 0.7681 (Cg_exo) REVERT: G 13 GLN cc_start: 0.7104 (tm-30) cc_final: 0.6490 (tm-30) REVERT: G 145 THR cc_start: 0.7737 (t) cc_final: 0.7479 (p) REVERT: G 166 GLN cc_start: 0.7188 (mm-40) cc_final: 0.6529 (tt0) REVERT: G 184 GLU cc_start: 0.7213 (tt0) cc_final: 0.6818 (tp30) REVERT: J 78 GLU cc_start: 0.6026 (tp30) cc_final: 0.5683 (mt-10) REVERT: J 102 GLU cc_start: 0.5507 (mm-30) cc_final: 0.4730 (tp30) REVERT: J 127 ASP cc_start: 0.5154 (OUTLIER) cc_final: 0.4460 (t0) REVERT: L 65 GLU cc_start: 0.5278 (pp20) cc_final: 0.3708 (tp30) REVERT: L 81 GLU cc_start: 0.7114 (pp20) cc_final: 0.6127 (mm-30) REVERT: L 82 GLU cc_start: 0.6018 (tp30) cc_final: 0.4774 (tt0) REVERT: L 141 GLU cc_start: 0.6117 (tt0) cc_final: 0.5395 (tp30) outliers start: 55 outliers final: 34 residues processed: 337 average time/residue: 0.4367 time to fit residues: 232.3467 Evaluate side-chains 326 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 281 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 0.9980 chunk 315 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 272 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 296 optimal weight: 0.4980 chunk 124 optimal weight: 6.9990 chunk 304 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN F 206 GLN ** F 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.131290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.106095 restraints weight = 46096.210| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.61 r_work: 0.3195 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3093 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= 0.199 Angle : 0.496 7.373 40807 Z= 0.250 Chirality : 0.043 0.198 4576 Planarity : 0.004 0.048 5333 Dihedral : 5.367 99.061 4231 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.75 % Allowed : 15.80 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.55 (0.14), residues: 3764 helix: 1.05 (0.14), residues: 1563 sheet: -0.50 (0.21), residues: 594 loop : 0.21 (0.17), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 424 HIS 0.004 0.001 HIS E 375 PHE 0.013 0.001 PHE G 108 TYR 0.014 0.001 TYR F 54 ARG 0.008 0.000 ARG B 488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6541.51 seconds wall clock time: 118 minutes 45.86 seconds (7125.86 seconds total)