Starting phenix.real_space_refine on Sun Mar 17 15:25:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbz_14597/03_2024/7zbz_14597.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbz_14597/03_2024/7zbz_14597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbz_14597/03_2024/7zbz_14597.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbz_14597/03_2024/7zbz_14597.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbz_14597/03_2024/7zbz_14597.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbz_14597/03_2024/7zbz_14597.pdb" } resolution = 3.1 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= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 101 5.16 5 C 11520 2.51 5 N 3118 2.21 5 O 3414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C GLU 194": "OE1" <-> "OE2" Residue "C PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 271": "OE1" <-> "OE2" Residue "C GLU 306": "OE1" <-> "OE2" Residue "C GLU 560": "OE1" <-> "OE2" Residue "C GLU 589": "OE1" <-> "OE2" Residue "C ASP 706": "OD1" <-> "OD2" Residue "D ASP 44": "OD1" <-> "OD2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D ASP 267": "OD1" <-> "OD2" Residue "D ASP 393": "OD1" <-> "OD2" Residue "D GLU 863": "OE1" <-> "OE2" Residue "D TYR 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 941": "OE1" <-> "OE2" Residue "D TYR 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18156 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 5846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5846 Classifications: {'peptide': 720} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 707} Chain breaks: 4 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 8845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1141, 8845 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 52, 'TRANS': 1088} Chain breaks: 5 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "R" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 713 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "S" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1033 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "F" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 1716 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 240} Link IDs: {'PTRANS': 13, 'TRANS': 300} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 803 Unresolved non-hydrogen angles: 1030 Unresolved non-hydrogen dihedrals: 648 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 13, 'TYR:plan': 3, 'ASN:plan1': 14, 'TRP:plan': 2, 'HIS:plan': 10, 'PHE:plan': 11, 'GLU:plan': 13, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 408 Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14879 SG CYS R 42 133.680 56.736 48.066 1.00 79.00 S ATOM 14898 SG CYS R 45 136.275 55.032 50.601 1.00 81.82 S ATOM 15193 SG CYS R 83 133.385 56.988 51.863 1.00 68.21 S ATOM 15122 SG CYS R 75 125.646 64.042 40.976 1.00 50.84 S ATOM 15289 SG CYS R 94 129.020 64.738 42.879 1.00 59.13 S ATOM 14965 SG CYS R 53 132.122 54.091 54.272 1.00 89.56 S ATOM 14988 SG CYS R 56 132.048 52.494 57.739 1.00 92.42 S ATOM 15072 SG CYS R 68 129.797 51.170 54.779 1.00 81.95 S Time building chain proxies: 10.04, per 1000 atoms: 0.55 Number of scatterers: 18156 At special positions: 0 Unit cell: (148.109, 156.621, 118.317, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 101 16.00 O 3414 8.00 N 3118 7.00 C 11520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.90 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " Number of angles added : 6 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4612 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 9 sheets defined 73.6% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'C' and resid 16 through 32 removed outlier: 3.907A pdb=" N ILE C 20 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP C 22 " --> pdb=" O ASP C 18 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ASP C 23 " --> pdb=" O GLN C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 55 removed outlier: 3.502A pdb=" N TYR C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 107 removed outlier: 3.710A pdb=" N LYS C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP C 106 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 137 removed outlier: 3.858A pdb=" N LEU C 116 " --> pdb=" O ASP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 143 removed outlier: 3.626A pdb=" N ASN C 141 " --> pdb=" O CYS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 152 removed outlier: 3.505A pdb=" N GLY C 152 " --> pdb=" O GLU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'C' and resid 171 through 193 removed outlier: 3.667A pdb=" N LEU C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LYS C 177 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLN C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 212 removed outlier: 3.770A pdb=" N GLY C 212 " --> pdb=" O TYR C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 232 through 255 removed outlier: 3.645A pdb=" N GLN C 253 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 279 removed outlier: 3.611A pdb=" N LYS C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 283 through 297 Processing helix chain 'C' and resid 299 through 313 Processing helix chain 'C' and resid 315 through 327 Processing helix chain 'C' and resid 333 through 356 removed outlier: 4.036A pdb=" N CYS C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY C 356 " --> pdb=" O ILE C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 362 through 385 Processing helix chain 'C' and resid 388 through 405 removed outlier: 3.753A pdb=" N ASN C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 416 through 431 removed outlier: 3.627A pdb=" N GLU C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 454 removed outlier: 3.588A pdb=" N LYS C 454 " --> pdb=" O MET C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 477 removed outlier: 4.200A pdb=" N PHE C 462 " --> pdb=" O ASP C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 496 removed outlier: 3.677A pdb=" N GLU C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 528 removed outlier: 3.630A pdb=" N MET C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR C 526 " --> pdb=" O LYS C 522 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN C 527 " --> pdb=" O LYS C 523 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER C 528 " --> pdb=" O HIS C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 558 No H-bonds generated for 'chain 'C' and resid 556 through 558' Processing helix chain 'C' and resid 559 through 574 Processing helix chain 'C' and resid 605 through 613 removed outlier: 3.575A pdb=" N GLN C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 630 Processing helix chain 'C' and resid 632 through 646 Processing helix chain 'C' and resid 688 through 722 removed outlier: 4.336A pdb=" N GLN C 692 " --> pdb=" O MET C 688 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS C 693 " --> pdb=" O LYS C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 739 removed outlier: 3.663A pdb=" N LEU C 730 " --> pdb=" O LYS C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 759 Processing helix chain 'D' and resid 6 through 15 Processing helix chain 'D' and resid 19 through 36 Processing helix chain 'D' and resid 43 through 57 removed outlier: 3.966A pdb=" N ARG D 47 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 79 removed outlier: 4.002A pdb=" N GLY D 73 " --> pdb=" O VAL D 69 " (cutoff:3.500A) Proline residue: D 74 - end of helix removed outlier: 4.471A pdb=" N SER D 77 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS D 78 " --> pdb=" O PRO D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 96 removed outlier: 3.877A pdb=" N VAL D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR D 86 " --> pdb=" O TYR D 82 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 96 " --> pdb=" O CYS D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 116 Processing helix chain 'D' and resid 128 through 144 removed outlier: 3.681A pdb=" N LYS D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 164 removed outlier: 3.874A pdb=" N GLN D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 171 removed outlier: 4.008A pdb=" N LEU D 168 " --> pdb=" O GLN D 165 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 169 " --> pdb=" O GLY D 166 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL D 170 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASN D 171 " --> pdb=" O LEU D 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 165 through 171' Processing helix chain 'D' and resid 172 through 181 removed outlier: 3.551A pdb=" N CYS D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 186 removed outlier: 3.728A pdb=" N THR D 185 " --> pdb=" O PRO D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 205 removed outlier: 3.566A pdb=" N ARG D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 224 removed outlier: 3.752A pdb=" N PHE D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 245 removed outlier: 3.623A pdb=" N ARG D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 251 removed outlier: 4.508A pdb=" N GLU D 251 " --> pdb=" O ARG D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 265 Proline residue: D 258 - end of helix removed outlier: 3.835A pdb=" N ASN D 265 " --> pdb=" O VAL D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 286 removed outlier: 3.601A pdb=" N ARG D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 292 No H-bonds generated for 'chain 'D' and resid 290 through 292' Processing helix chain 'D' and resid 293 through 305 Processing helix chain 'D' and resid 346 through 364 removed outlier: 4.000A pdb=" N ARG D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 382 removed outlier: 4.940A pdb=" N SER D 376 " --> pdb=" O TYR D 372 " (cutoff:3.500A) Proline residue: D 377 - end of helix Processing helix chain 'D' and resid 383 through 385 No H-bonds generated for 'chain 'D' and resid 383 through 385' Processing helix chain 'D' and resid 387 through 406 removed outlier: 3.579A pdb=" N ARG D 406 " --> pdb=" O LEU D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 443 Proline residue: D 433 - end of helix removed outlier: 3.794A pdb=" N LYS D 441 " --> pdb=" O LYS D 437 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 465 removed outlier: 3.692A pdb=" N ARG D 451 " --> pdb=" O SER D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 Proline residue: D 478 - end of helix Processing helix chain 'D' and resid 490 through 507 Processing helix chain 'D' and resid 508 through 515 removed outlier: 6.177A pdb=" N GLN D 511 " --> pdb=" O HIS D 508 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS D 514 " --> pdb=" O GLN D 511 " (cutoff:3.500A) Proline residue: D 515 - end of helix Processing helix chain 'D' and resid 516 through 529 Proline residue: D 522 - end of helix removed outlier: 3.640A pdb=" N GLY D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 551 removed outlier: 3.612A pdb=" N GLN D 545 " --> pdb=" O LEU D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 577 removed outlier: 3.576A pdb=" N ILE D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LYS D 566 " --> pdb=" O THR D 562 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP D 567 " --> pdb=" O PRO D 563 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 568 " --> pdb=" O TYR D 564 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS D 574 " --> pdb=" O THR D 570 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG D 575 " --> pdb=" O CYS D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 601 Processing helix chain 'D' and resid 606 through 621 removed outlier: 4.551A pdb=" N ASN D 610 " --> pdb=" O SER D 606 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS D 620 " --> pdb=" O LEU D 616 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN D 621 " --> pdb=" O GLU D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 637 Processing helix chain 'D' and resid 644 through 658 removed outlier: 3.505A pdb=" N GLY D 649 " --> pdb=" O ARG D 645 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU D 650 " --> pdb=" O PRO D 646 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL D 652 " --> pdb=" O LEU D 648 " (cutoff:3.500A) Proline residue: D 653 - end of helix Processing helix chain 'D' and resid 659 through 661 No H-bonds generated for 'chain 'D' and resid 659 through 661' Processing helix chain 'D' and resid 663 through 681 Processing helix chain 'D' and resid 686 through 695 Processing helix chain 'D' and resid 705 through 723 removed outlier: 3.625A pdb=" N SER D 709 " --> pdb=" O ASP D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 731 removed outlier: 4.325A pdb=" N SER D 728 " --> pdb=" O SER D 725 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 730 " --> pdb=" O LEU D 727 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER D 731 " --> pdb=" O SER D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 743 removed outlier: 3.660A pdb=" N ASN D 736 " --> pdb=" O GLY D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 766 removed outlier: 3.832A pdb=" N VAL D 764 " --> pdb=" O GLN D 760 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR D 765 " --> pdb=" O ALA D 761 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 786 Proline residue: D 782 - end of helix Processing helix chain 'D' and resid 793 through 810 removed outlier: 4.137A pdb=" N TYR D 797 " --> pdb=" O LYS D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 827 Processing helix chain 'D' and resid 831 through 849 removed outlier: 4.381A pdb=" N HIS D 848 " --> pdb=" O GLU D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 866 removed outlier: 4.070A pdb=" N SER D 866 " --> pdb=" O LEU D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 887 Processing helix chain 'D' and resid 887 through 902 Proline residue: D 893 - end of helix removed outlier: 3.838A pdb=" N THR D 900 " --> pdb=" O LEU D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 905 through 919 removed outlier: 3.624A pdb=" N LEU D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 921 through 926 Processing helix chain 'D' and resid 928 through 940 Processing helix chain 'D' and resid 947 through 960 removed outlier: 3.724A pdb=" N LEU D 960 " --> pdb=" O GLY D 956 " (cutoff:3.500A) Processing helix chain 'D' and resid 962 through 976 removed outlier: 3.925A pdb=" N LEU D 966 " --> pdb=" O ASP D 962 " (cutoff:3.500A) Proline residue: D 968 - end of helix removed outlier: 3.735A pdb=" N TYR D 973 " --> pdb=" O ARG D 969 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU D 974 " --> pdb=" O LEU D 970 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE D 975 " --> pdb=" O LYS D 971 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER D 976 " --> pdb=" O GLY D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 990 removed outlier: 3.666A pdb=" N ARG D 982 " --> pdb=" O SER D 978 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER D 983 " --> pdb=" O SER D 979 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS D 990 " --> pdb=" O VAL D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 993 No H-bonds generated for 'chain 'D' and resid 991 through 993' Processing helix chain 'D' and resid 1000 through 1013 removed outlier: 5.084A pdb=" N GLY D1009 " --> pdb=" O LYS D1005 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASP D1010 " --> pdb=" O ASN D1006 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE D1011 " --> pdb=" O CYS D1007 " (cutoff:3.500A) Processing helix chain 'D' and resid 1014 through 1017 Processing helix chain 'D' and resid 1019 through 1037 removed outlier: 3.706A pdb=" N ARG D1023 " --> pdb=" O ASP D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1041 Processing helix chain 'D' and resid 1044 through 1055 Proline residue: D1050 - end of helix removed outlier: 3.554A pdb=" N GLU D1055 " --> pdb=" O HIS D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1059 through 1063 Processing helix chain 'D' and resid 1078 through 1096 Processing helix chain 'D' and resid 1101 through 1113 removed outlier: 3.723A pdb=" N PHE D1105 " --> pdb=" O ASP D1101 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1133 removed outlier: 3.993A pdb=" N THR D1132 " --> pdb=" O VAL D1128 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D1133 " --> pdb=" O ARG D1129 " (cutoff:3.500A) Processing helix chain 'D' and resid 1134 through 1141 removed outlier: 4.250A pdb=" N VAL D1138 " --> pdb=" O CYS D1134 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG D1141 " --> pdb=" O ALA D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1146 through 1154 Processing helix chain 'D' and resid 1162 through 1185 removed outlier: 3.754A pdb=" N PHE D1166 " --> pdb=" O VAL D1162 " (cutoff:3.500A) Processing helix chain 'D' and resid 1194 through 1205 Processing helix chain 'D' and resid 1205 through 1216 Processing helix chain 'R' and resid 53 through 59 Processing helix chain 'R' and resid 62 through 67 removed outlier: 3.761A pdb=" N GLU R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 88 Processing helix chain 'S' and resid 18 through 22 Processing helix chain 'S' and resid 24 through 33 Processing helix chain 'S' and resid 51 through 65 removed outlier: 3.538A pdb=" N LYS S 57 " --> pdb=" O ALA S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 94 Processing helix chain 'S' and resid 96 through 111 Processing helix chain 'S' and resid 112 through 128 Processing helix chain 'S' and resid 131 through 140 removed outlier: 3.624A pdb=" N ILE S 135 " --> pdb=" O THR S 131 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 156 removed outlier: 3.754A pdb=" N GLU S 156 " --> pdb=" O GLN S 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 100 Processing helix chain 'F' and resid 101 through 110 removed outlier: 3.663A pdb=" N LEU F 105 " --> pdb=" O PRO F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 121 Processing helix chain 'F' and resid 124 through 132 removed outlier: 3.697A pdb=" N SER F 132 " --> pdb=" O TYR F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 158 Processing helix chain 'F' and resid 194 through 203 Processing helix chain 'F' and resid 219 through 227 Processing helix chain 'F' and resid 244 through 255 Processing helix chain 'F' and resid 270 through 280 Processing helix chain 'F' and resid 298 through 309 Processing helix chain 'F' and resid 324 through 334 removed outlier: 3.521A pdb=" N LEU F 334 " --> pdb=" O GLU F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 359 removed outlier: 3.539A pdb=" N LEU F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 383 removed outlier: 3.878A pdb=" N LEU F 378 " --> pdb=" O GLY F 374 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 534 through 541 removed outlier: 7.559A pdb=" N PHE R 22 " --> pdb=" O LEU C 590 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N LEU C 590 " --> pdb=" O PHE R 22 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N VAL R 24 " --> pdb=" O GLY C 588 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N GLY C 588 " --> pdb=" O VAL R 24 " (cutoff:3.500A) removed outlier: 11.523A pdb=" N LYS R 26 " --> pdb=" O SER C 586 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N SER C 586 " --> pdb=" O LYS R 26 " (cutoff:3.500A) removed outlier: 11.391A pdb=" N ASN R 28 " --> pdb=" O GLN C 584 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N GLN C 584 " --> pdb=" O ASN R 28 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL R 30 " --> pdb=" O LEU C 582 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR C 599 " --> pdb=" O THR C 592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 619 through 621 Processing sheet with id=AA3, first strand: chain 'C' and resid 724 through 725 Processing sheet with id=AA4, first strand: chain 'R' and resid 79 through 80 removed outlier: 6.667A pdb=" N TRP R 72 " --> pdb=" O GLN R 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 13 through 17 removed outlier: 9.331A pdb=" N VAL S 45 " --> pdb=" O SER S 3 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LYS S 5 " --> pdb=" O VAL S 45 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 139 through 141 removed outlier: 3.906A pdb=" N MET F 186 " --> pdb=" O ASN F 210 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER F 212 " --> pdb=" O MET F 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AA8, first strand: chain 'F' and resid 260 through 262 Processing sheet with id=AA9, first strand: chain 'F' and resid 339 through 341 1148 hydrogen bonds defined for protein. 3369 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.34 Time building geometry restraints manager: 7.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5985 1.34 - 1.46: 2337 1.46 - 1.58: 9968 1.58 - 1.69: 0 1.69 - 1.81: 147 Bond restraints: 18437 Sorted by residual: bond pdb=" CG1 ILE D 241 " pdb=" CD1 ILE D 241 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.36e+00 bond pdb=" C SER F 179 " pdb=" N PRO F 180 " ideal model delta sigma weight residual 1.331 1.345 -0.013 1.27e-02 6.20e+03 1.12e+00 bond pdb=" N MET D 15 " pdb=" CA MET D 15 " ideal model delta sigma weight residual 1.458 1.472 -0.014 1.42e-02 4.96e+03 1.00e+00 bond pdb=" C LEU D 888 " pdb=" N PRO D 889 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.38e-02 5.25e+03 9.51e-01 bond pdb=" CG LEU D 181 " pdb=" CD1 LEU D 181 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 9.11e-01 ... (remaining 18432 not shown) Histogram of bond angle deviations from ideal: 99.05 - 106.05: 328 106.05 - 113.04: 10310 113.04 - 120.04: 6281 120.04 - 127.03: 7924 127.03 - 134.03: 155 Bond angle restraints: 24998 Sorted by residual: angle pdb=" N GLU D1171 " pdb=" CA GLU D1171 " pdb=" CB GLU D1171 " ideal model delta sigma weight residual 110.28 115.65 -5.37 1.55e+00 4.16e-01 1.20e+01 angle pdb=" N GLU C 705 " pdb=" CA GLU C 705 " pdb=" CB GLU C 705 " ideal model delta sigma weight residual 110.16 115.24 -5.08 1.48e+00 4.57e-01 1.18e+01 angle pdb=" C LYS D 661 " pdb=" N ASN D 662 " pdb=" CA ASN D 662 " ideal model delta sigma weight residual 121.54 127.42 -5.88 1.91e+00 2.74e-01 9.46e+00 angle pdb=" CA LYS D 793 " pdb=" CB LYS D 793 " pdb=" CG LYS D 793 " ideal model delta sigma weight residual 114.10 119.94 -5.84 2.00e+00 2.50e-01 8.54e+00 angle pdb=" CA LEU D 177 " pdb=" CB LEU D 177 " pdb=" CG LEU D 177 " ideal model delta sigma weight residual 116.30 126.52 -10.22 3.50e+00 8.16e-02 8.53e+00 ... (remaining 24993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10220 17.97 - 35.95: 890 35.95 - 53.92: 159 53.92 - 71.89: 18 71.89 - 89.87: 9 Dihedral angle restraints: 11296 sinusoidal: 4240 harmonic: 7056 Sorted by residual: dihedral pdb=" CA MET C 111 " pdb=" C MET C 111 " pdb=" N ASP C 112 " pdb=" CA ASP C 112 " ideal model delta harmonic sigma weight residual -180.00 -158.84 -21.16 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLU D 221 " pdb=" C GLU D 221 " pdb=" N LEU D 222 " pdb=" CA LEU D 222 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA TYR C 32 " pdb=" C TYR C 32 " pdb=" N THR C 33 " pdb=" CA THR C 33 " ideal model delta harmonic sigma weight residual 180.00 163.23 16.77 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 11293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2205 0.040 - 0.079: 601 0.079 - 0.119: 164 0.119 - 0.159: 12 0.159 - 0.198: 2 Chirality restraints: 2984 Sorted by residual: chirality pdb=" CA LEU D 181 " pdb=" N LEU D 181 " pdb=" C LEU D 181 " pdb=" CB LEU D 181 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CA GLU D 221 " pdb=" N GLU D 221 " pdb=" C GLU D 221 " pdb=" CB GLU D 221 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.48e-01 chirality pdb=" CA GLU S 102 " pdb=" N GLU S 102 " pdb=" C GLU S 102 " pdb=" CB GLU S 102 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 2981 not shown) Planarity restraints: 3186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 888 " -0.064 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO D 889 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO D 889 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 889 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 181 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO D 182 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 182 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 182 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 555 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO C 556 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 556 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 556 " -0.026 5.00e-02 4.00e+02 ... (remaining 3183 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 79 2.57 - 3.15: 14324 3.15 - 3.74: 27623 3.74 - 4.32: 35083 4.32 - 4.90: 61547 Nonbonded interactions: 138656 Sorted by model distance: nonbonded pdb=" OD2 ASP R 97 " pdb="ZN ZN R 202 " model vdw 1.989 2.230 nonbonded pdb=" OD1 ASP D 691 " pdb=" NZ LYS D 729 " model vdw 2.251 2.520 nonbonded pdb=" OH TYR D 372 " pdb=" OG1 THR D 405 " model vdw 2.256 2.440 nonbonded pdb=" OE1 GLU D 617 " pdb=" NH1 ARG D 618 " model vdw 2.270 2.520 nonbonded pdb=" O PRO S 86 " pdb=" N ASP S 89 " model vdw 2.288 2.520 ... (remaining 138651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 7.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 9.040 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 53.700 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18437 Z= 0.168 Angle : 0.519 10.221 24998 Z= 0.273 Chirality : 0.039 0.198 2984 Planarity : 0.004 0.095 3186 Dihedral : 13.596 89.868 6684 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.18), residues: 2360 helix: 2.22 (0.14), residues: 1548 sheet: -2.54 (0.54), residues: 81 loop : -0.88 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 33 HIS 0.003 0.001 HIS C 727 PHE 0.020 0.001 PHE C 402 TYR 0.019 0.001 TYR C 50 ARG 0.009 0.000 ARG C 764 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 453 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 146 ARG cc_start: 0.7374 (tmm160) cc_final: 0.7171 (ttp80) REVERT: C 375 LYS cc_start: 0.8228 (ttmt) cc_final: 0.8007 (ttpp) REVERT: C 510 ASP cc_start: 0.8121 (m-30) cc_final: 0.7710 (m-30) REVERT: C 519 GLU cc_start: 0.7134 (tp30) cc_final: 0.6908 (tp30) REVERT: C 578 LYS cc_start: 0.8303 (ptmt) cc_final: 0.8072 (ptmm) REVERT: C 641 GLN cc_start: 0.7472 (tm-30) cc_final: 0.6797 (tm-30) REVERT: C 642 ILE cc_start: 0.8487 (mm) cc_final: 0.8284 (mm) REVERT: C 645 LYS cc_start: 0.7975 (mmtt) cc_final: 0.7156 (mmtt) REVERT: D 51 LYS cc_start: 0.7366 (mtmt) cc_final: 0.6930 (mtmt) REVERT: D 52 MET cc_start: 0.6959 (tpp) cc_final: 0.6600 (tpp) REVERT: D 104 ASP cc_start: 0.7593 (p0) cc_final: 0.7147 (p0) REVERT: D 216 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6475 (mm-30) REVERT: D 705 ASP cc_start: 0.6961 (t70) cc_final: 0.6704 (t0) REVERT: D 863 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7134 (tm-30) REVERT: D 962 ASP cc_start: 0.7062 (t0) cc_final: 0.6827 (t0) REVERT: D 1003 LEU cc_start: 0.8205 (mt) cc_final: 0.7789 (mp) REVERT: D 1007 CYS cc_start: 0.7623 (p) cc_final: 0.7259 (p) REVERT: D 1171 GLU cc_start: 0.6916 (mp0) cc_final: 0.6362 (mp0) REVERT: R 50 MET cc_start: 0.6854 (mtm) cc_final: 0.6614 (mtm) REVERT: S 105 LEU cc_start: 0.8093 (mm) cc_final: 0.7890 (mt) REVERT: F 116 GLU cc_start: 0.7044 (mp0) cc_final: 0.6719 (mp0) REVERT: F 126 ARG cc_start: 0.7675 (ttt-90) cc_final: 0.7340 (ttt180) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.3448 time to fit residues: 225.5384 Evaluate side-chains 410 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 100 optimal weight: 0.2980 chunk 61 optimal weight: 10.0000 chunk 121 optimal weight: 0.0770 chunk 96 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 138 optimal weight: 0.0070 chunk 216 optimal weight: 20.0000 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 18437 Z= 0.158 Angle : 0.489 7.927 24998 Z= 0.253 Chirality : 0.038 0.139 2984 Planarity : 0.004 0.062 3186 Dihedral : 3.428 20.152 2539 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.00 % Allowed : 9.62 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.18), residues: 2360 helix: 2.37 (0.13), residues: 1574 sheet: -1.90 (0.64), residues: 71 loop : -0.59 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 33 HIS 0.003 0.001 HIS D 939 PHE 0.024 0.001 PHE D 211 TYR 0.019 0.001 TYR C 563 ARG 0.006 0.000 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 408 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 375 LYS cc_start: 0.8279 (ttmt) cc_final: 0.8034 (ttpp) REVERT: C 519 GLU cc_start: 0.7172 (tp30) cc_final: 0.6863 (tp30) REVERT: C 578 LYS cc_start: 0.8301 (ptmt) cc_final: 0.8092 (ptmm) REVERT: C 620 TYR cc_start: 0.6761 (m-80) cc_final: 0.6258 (m-80) REVERT: C 641 GLN cc_start: 0.7535 (tm-30) cc_final: 0.6679 (tm-30) REVERT: C 642 ILE cc_start: 0.8391 (mm) cc_final: 0.8142 (mm) REVERT: C 645 LYS cc_start: 0.7750 (mmtt) cc_final: 0.6721 (mmtt) REVERT: C 705 GLU cc_start: 0.6635 (mp0) cc_final: 0.5991 (mp0) REVERT: D 51 LYS cc_start: 0.7422 (mtmt) cc_final: 0.6993 (mtmt) REVERT: D 104 ASP cc_start: 0.7620 (p0) cc_final: 0.7189 (p0) REVERT: D 147 ASP cc_start: 0.6719 (t0) cc_final: 0.6402 (t0) REVERT: D 216 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6569 (mm-30) REVERT: D 398 TYR cc_start: 0.8496 (t80) cc_final: 0.7970 (t80) REVERT: D 705 ASP cc_start: 0.6981 (t70) cc_final: 0.6724 (t0) REVERT: D 863 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7091 (tm-30) REVERT: D 962 ASP cc_start: 0.7102 (t0) cc_final: 0.6834 (t0) REVERT: D 973 TYR cc_start: 0.8165 (m-80) cc_final: 0.7870 (m-80) REVERT: D 1003 LEU cc_start: 0.8263 (mt) cc_final: 0.7763 (mp) REVERT: D 1005 LYS cc_start: 0.8657 (tptp) cc_final: 0.8407 (tptt) REVERT: D 1007 CYS cc_start: 0.7673 (p) cc_final: 0.7209 (p) REVERT: D 1131 SER cc_start: 0.7941 (m) cc_final: 0.7615 (t) REVERT: R 50 MET cc_start: 0.6865 (mtm) cc_final: 0.6628 (mtm) REVERT: F 116 GLU cc_start: 0.7066 (mp0) cc_final: 0.6691 (mp0) outliers start: 19 outliers final: 10 residues processed: 411 average time/residue: 0.3372 time to fit residues: 201.1072 Evaluate side-chains 414 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 404 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 760 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain D residue 1093 LEU Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 179 optimal weight: 0.6980 chunk 147 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 216 optimal weight: 20.0000 chunk 233 optimal weight: 50.0000 chunk 192 optimal weight: 2.9990 chunk 214 optimal weight: 10.0000 chunk 73 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 HIS D 277 GLN D 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 18437 Z= 0.200 Angle : 0.487 8.246 24998 Z= 0.251 Chirality : 0.038 0.135 2984 Planarity : 0.004 0.048 3186 Dihedral : 3.438 19.902 2539 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.69 % Allowed : 12.00 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.18), residues: 2360 helix: 2.44 (0.13), residues: 1568 sheet: -1.49 (0.71), residues: 61 loop : -0.64 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 33 HIS 0.005 0.001 HIS D 707 PHE 0.023 0.001 PHE C 402 TYR 0.018 0.001 TYR C 563 ARG 0.003 0.000 ARG C 764 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 422 time to evaluate : 2.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 519 GLU cc_start: 0.7205 (tp30) cc_final: 0.6951 (tp30) REVERT: C 578 LYS cc_start: 0.8280 (ptmt) cc_final: 0.8060 (ptmm) REVERT: C 589 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6470 (mm-30) REVERT: C 620 TYR cc_start: 0.6760 (m-80) cc_final: 0.6218 (m-80) REVERT: C 641 GLN cc_start: 0.7565 (tm-30) cc_final: 0.6767 (tm-30) REVERT: C 642 ILE cc_start: 0.8433 (mm) cc_final: 0.8121 (mm) REVERT: C 645 LYS cc_start: 0.7777 (mmtt) cc_final: 0.6898 (mmtt) REVERT: D 51 LYS cc_start: 0.7482 (mtmt) cc_final: 0.7052 (mtmt) REVERT: D 104 ASP cc_start: 0.7609 (p0) cc_final: 0.7161 (p0) REVERT: D 216 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6662 (mm-30) REVERT: D 705 ASP cc_start: 0.7024 (t70) cc_final: 0.6765 (t0) REVERT: D 863 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7089 (tm-30) REVERT: D 962 ASP cc_start: 0.7091 (t0) cc_final: 0.6870 (t0) REVERT: D 1003 LEU cc_start: 0.8373 (mt) cc_final: 0.7838 (mp) REVERT: D 1007 CYS cc_start: 0.7672 (p) cc_final: 0.7224 (p) REVERT: D 1059 ARG cc_start: 0.7278 (mtp85) cc_final: 0.6945 (mtp85) REVERT: D 1118 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6740 (m-30) REVERT: D 1131 SER cc_start: 0.8051 (m) cc_final: 0.7836 (m) REVERT: D 1171 GLU cc_start: 0.6946 (mp0) cc_final: 0.6439 (mp0) REVERT: R 50 MET cc_start: 0.6838 (mtm) cc_final: 0.6611 (mtm) REVERT: S 55 LEU cc_start: 0.8597 (tp) cc_final: 0.8330 (tt) REVERT: S 96 ASP cc_start: 0.5757 (OUTLIER) cc_final: 0.5506 (p0) REVERT: S 102 GLU cc_start: 0.6743 (mp0) cc_final: 0.6242 (mp0) REVERT: F 116 GLU cc_start: 0.7118 (mp0) cc_final: 0.6748 (mp0) outliers start: 32 outliers final: 16 residues processed: 434 average time/residue: 0.3422 time to fit residues: 216.1727 Evaluate side-chains 433 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 415 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 503 LYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 760 GLU Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1093 LEU Chi-restraints excluded: chain D residue 1118 ASP Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 96 ASP Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 0.0370 chunk 162 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 230 optimal weight: 9.9990 chunk 113 optimal weight: 0.5980 chunk 205 optimal weight: 1.9990 chunk 61 optimal weight: 0.0970 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 HIS C 524 HIS D 277 GLN D 599 ASN D1169 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 18437 Z= 0.161 Angle : 0.467 8.066 24998 Z= 0.241 Chirality : 0.037 0.135 2984 Planarity : 0.004 0.047 3186 Dihedral : 3.376 19.648 2539 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.90 % Allowed : 13.00 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.18), residues: 2360 helix: 2.51 (0.13), residues: 1567 sheet: -1.38 (0.72), residues: 61 loop : -0.63 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 33 HIS 0.007 0.001 HIS C 524 PHE 0.019 0.001 PHE C 402 TYR 0.017 0.001 TYR C 563 ARG 0.003 0.000 ARG C 764 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 417 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 375 LYS cc_start: 0.8291 (ttmt) cc_final: 0.8053 (ttpp) REVERT: C 519 GLU cc_start: 0.7167 (tp30) cc_final: 0.6936 (tp30) REVERT: C 578 LYS cc_start: 0.8273 (ptmt) cc_final: 0.8057 (ptmm) REVERT: C 589 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6307 (mm-30) REVERT: C 620 TYR cc_start: 0.6780 (m-80) cc_final: 0.6200 (m-80) REVERT: C 641 GLN cc_start: 0.7555 (tm-30) cc_final: 0.6762 (tm-30) REVERT: C 642 ILE cc_start: 0.8431 (mm) cc_final: 0.8104 (mm) REVERT: C 645 LYS cc_start: 0.7784 (mmtt) cc_final: 0.6860 (mmtt) REVERT: D 52 MET cc_start: 0.6967 (tpp) cc_final: 0.6622 (tpp) REVERT: D 104 ASP cc_start: 0.7586 (p0) cc_final: 0.7163 (p0) REVERT: D 216 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6761 (mm-30) REVERT: D 221 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6819 (mp0) REVERT: D 705 ASP cc_start: 0.7034 (t70) cc_final: 0.6779 (t0) REVERT: D 823 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7919 (mp10) REVERT: D 962 ASP cc_start: 0.7075 (t0) cc_final: 0.6844 (t0) REVERT: D 1003 LEU cc_start: 0.8376 (mt) cc_final: 0.7834 (mp) REVERT: D 1007 CYS cc_start: 0.7637 (p) cc_final: 0.7194 (p) REVERT: D 1131 SER cc_start: 0.7995 (m) cc_final: 0.7641 (t) REVERT: D 1171 GLU cc_start: 0.6927 (mp0) cc_final: 0.6421 (mp0) REVERT: D 1212 PHE cc_start: 0.8073 (t80) cc_final: 0.7745 (t80) REVERT: R 50 MET cc_start: 0.6851 (mtm) cc_final: 0.6621 (mtm) REVERT: S 32 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6553 (mt-10) REVERT: S 55 LEU cc_start: 0.8570 (tp) cc_final: 0.8288 (tt) REVERT: S 96 ASP cc_start: 0.5777 (OUTLIER) cc_final: 0.5527 (p0) REVERT: S 102 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6289 (mp0) REVERT: S 103 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7625 (tt) REVERT: F 116 GLU cc_start: 0.7145 (mp0) cc_final: 0.6838 (mp0) outliers start: 36 outliers final: 21 residues processed: 432 average time/residue: 0.3349 time to fit residues: 210.4633 Evaluate side-chains 437 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 412 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 760 GLU Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain D residue 403 LYS Chi-restraints excluded: chain D residue 599 ASN Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 824 ASP Chi-restraints excluded: chain D residue 1093 LEU Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 96 ASP Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 0.0060 chunk 130 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 196 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 GLN D1169 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 18437 Z= 0.219 Angle : 0.492 9.372 24998 Z= 0.253 Chirality : 0.039 0.137 2984 Planarity : 0.004 0.047 3186 Dihedral : 3.431 19.698 2539 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.01 % Allowed : 14.22 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.18), residues: 2360 helix: 2.45 (0.13), residues: 1568 sheet: -1.19 (0.72), residues: 61 loop : -0.65 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 33 HIS 0.005 0.001 HIS D 707 PHE 0.023 0.001 PHE C 402 TYR 0.021 0.002 TYR C 50 ARG 0.003 0.000 ARG C 764 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 419 time to evaluate : 2.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 375 LYS cc_start: 0.8280 (ttmt) cc_final: 0.8022 (ttpp) REVERT: C 519 GLU cc_start: 0.7204 (tp30) cc_final: 0.6947 (tp30) REVERT: C 578 LYS cc_start: 0.8270 (ptmt) cc_final: 0.8052 (ptmm) REVERT: C 589 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6287 (mm-30) REVERT: C 620 TYR cc_start: 0.6779 (m-80) cc_final: 0.6169 (m-80) REVERT: C 641 GLN cc_start: 0.7589 (tm-30) cc_final: 0.6776 (tm-30) REVERT: C 642 ILE cc_start: 0.8456 (mm) cc_final: 0.8131 (mm) REVERT: C 645 LYS cc_start: 0.7807 (mmtt) cc_final: 0.6871 (mmtt) REVERT: D 51 LYS cc_start: 0.7500 (mtmt) cc_final: 0.7098 (mtmt) REVERT: D 52 MET cc_start: 0.6870 (tpp) cc_final: 0.6302 (tpp) REVERT: D 104 ASP cc_start: 0.7599 (p0) cc_final: 0.7190 (p0) REVERT: D 147 ASP cc_start: 0.6634 (t0) cc_final: 0.6298 (t70) REVERT: D 156 ASP cc_start: 0.7056 (t70) cc_final: 0.6805 (t70) REVERT: D 216 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6762 (mm-30) REVERT: D 221 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: D 705 ASP cc_start: 0.7088 (t70) cc_final: 0.6826 (t0) REVERT: D 823 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7958 (mp10) REVERT: D 962 ASP cc_start: 0.7054 (t0) cc_final: 0.6736 (t0) REVERT: D 965 THR cc_start: 0.8651 (t) cc_final: 0.8121 (t) REVERT: D 1003 LEU cc_start: 0.8435 (mt) cc_final: 0.7876 (mp) REVERT: D 1007 CYS cc_start: 0.7646 (p) cc_final: 0.7209 (p) REVERT: D 1059 ARG cc_start: 0.7248 (mtp85) cc_final: 0.6936 (mtp85) REVERT: D 1171 GLU cc_start: 0.6960 (mp0) cc_final: 0.6402 (mp0) REVERT: D 1212 PHE cc_start: 0.8089 (t80) cc_final: 0.7780 (t80) REVERT: R 50 MET cc_start: 0.6833 (mtm) cc_final: 0.6614 (mtm) REVERT: S 32 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6577 (mt-10) REVERT: S 55 LEU cc_start: 0.8588 (tp) cc_final: 0.8308 (tt) REVERT: S 96 ASP cc_start: 0.5833 (OUTLIER) cc_final: 0.5577 (p0) REVERT: S 102 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6250 (mp0) REVERT: S 103 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7603 (tt) REVERT: S 135 ILE cc_start: 0.5469 (OUTLIER) cc_final: 0.5017 (mt) REVERT: F 116 GLU cc_start: 0.7241 (mp0) cc_final: 0.6933 (mp0) outliers start: 38 outliers final: 26 residues processed: 435 average time/residue: 0.3478 time to fit residues: 218.6385 Evaluate side-chains 440 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 409 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 503 LYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain D residue 403 LYS Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1093 LEU Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 96 ASP Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 135 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 157 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 230 optimal weight: 9.9990 chunk 191 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 GLN D1169 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18437 Z= 0.276 Angle : 0.523 10.472 24998 Z= 0.270 Chirality : 0.040 0.145 2984 Planarity : 0.004 0.047 3186 Dihedral : 3.571 20.740 2539 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.54 % Allowed : 13.95 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.18), residues: 2360 helix: 2.37 (0.13), residues: 1562 sheet: -1.09 (0.73), residues: 61 loop : -0.69 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 33 HIS 0.007 0.001 HIS D 707 PHE 0.024 0.002 PHE C 402 TYR 0.026 0.002 TYR C 50 ARG 0.005 0.000 ARG C 741 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 420 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 519 GLU cc_start: 0.7187 (tp30) cc_final: 0.6948 (tp30) REVERT: C 522 LYS cc_start: 0.7583 (tppp) cc_final: 0.7317 (tppt) REVERT: C 578 LYS cc_start: 0.8281 (ptmt) cc_final: 0.8053 (ptmm) REVERT: C 589 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6254 (mm-30) REVERT: C 620 TYR cc_start: 0.6722 (m-80) cc_final: 0.6101 (m-80) REVERT: C 641 GLN cc_start: 0.7614 (tm-30) cc_final: 0.6774 (tm-30) REVERT: C 642 ILE cc_start: 0.8528 (mm) cc_final: 0.8196 (mm) REVERT: C 645 LYS cc_start: 0.7870 (mmtt) cc_final: 0.6871 (mmtt) REVERT: D 51 LYS cc_start: 0.7520 (mtmt) cc_final: 0.7139 (mtmt) REVERT: D 104 ASP cc_start: 0.7599 (p0) cc_final: 0.7166 (p0) REVERT: D 147 ASP cc_start: 0.6800 (t0) cc_final: 0.6564 (t0) REVERT: D 216 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6843 (mm-30) REVERT: D 221 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: D 705 ASP cc_start: 0.7145 (t70) cc_final: 0.6887 (t0) REVERT: D 823 GLN cc_start: 0.8208 (mm-40) cc_final: 0.8003 (mp10) REVERT: D 962 ASP cc_start: 0.7052 (t0) cc_final: 0.6747 (t0) REVERT: D 965 THR cc_start: 0.8656 (t) cc_final: 0.8055 (t) REVERT: D 1003 LEU cc_start: 0.8486 (mt) cc_final: 0.7904 (mp) REVERT: D 1007 CYS cc_start: 0.7632 (p) cc_final: 0.7186 (p) REVERT: D 1059 ARG cc_start: 0.7293 (mtp85) cc_final: 0.7045 (mtp85) REVERT: D 1133 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7522 (pp) REVERT: D 1178 ARG cc_start: 0.8019 (ttm170) cc_final: 0.7717 (mtm-85) REVERT: D 1212 PHE cc_start: 0.8097 (t80) cc_final: 0.7774 (t80) REVERT: R 50 MET cc_start: 0.6851 (mtm) cc_final: 0.6637 (mtm) REVERT: S 32 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6646 (mt-10) REVERT: S 55 LEU cc_start: 0.8594 (tp) cc_final: 0.8307 (tt) REVERT: S 96 ASP cc_start: 0.5864 (OUTLIER) cc_final: 0.5619 (p0) REVERT: S 103 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7644 (tt) REVERT: F 116 GLU cc_start: 0.7346 (mp0) cc_final: 0.7030 (mp0) outliers start: 48 outliers final: 31 residues processed: 445 average time/residue: 0.3269 time to fit residues: 212.7930 Evaluate side-chains 451 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 416 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 503 LYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain D residue 403 LYS Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 738 LEU Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1093 LEU Chi-restraints excluded: chain D residue 1133 LEU Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 96 ASP Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 157 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 229 optimal weight: 50.0000 chunk 143 optimal weight: 0.1980 chunk 139 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 HIS D 277 GLN D 939 HIS D1169 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18437 Z= 0.190 Angle : 0.492 9.654 24998 Z= 0.255 Chirality : 0.038 0.137 2984 Planarity : 0.004 0.048 3186 Dihedral : 3.481 20.251 2539 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.17 % Allowed : 15.43 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.18), residues: 2360 helix: 2.43 (0.13), residues: 1566 sheet: -0.98 (0.73), residues: 61 loop : -0.67 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 33 HIS 0.004 0.001 HIS D1108 PHE 0.020 0.001 PHE C 402 TYR 0.025 0.001 TYR C 50 ARG 0.004 0.000 ARG C 741 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 407 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 519 GLU cc_start: 0.7189 (tp30) cc_final: 0.6949 (tp30) REVERT: C 522 LYS cc_start: 0.7517 (tppp) cc_final: 0.7278 (tppt) REVERT: C 578 LYS cc_start: 0.8293 (ptmt) cc_final: 0.8063 (ptmm) REVERT: C 589 GLU cc_start: 0.6859 (mm-30) cc_final: 0.6285 (mm-30) REVERT: C 610 ILE cc_start: 0.8423 (pt) cc_final: 0.8168 (mt) REVERT: C 620 TYR cc_start: 0.6723 (m-80) cc_final: 0.6160 (m-80) REVERT: C 641 GLN cc_start: 0.7577 (tm-30) cc_final: 0.6727 (tm-30) REVERT: C 642 ILE cc_start: 0.8484 (mm) cc_final: 0.8125 (mm) REVERT: C 645 LYS cc_start: 0.7807 (mmtt) cc_final: 0.6857 (mmtt) REVERT: C 706 ASP cc_start: 0.7082 (m-30) cc_final: 0.6741 (m-30) REVERT: D 51 LYS cc_start: 0.7494 (mtmt) cc_final: 0.7127 (mtmt) REVERT: D 104 ASP cc_start: 0.7576 (p0) cc_final: 0.7230 (p0) REVERT: D 147 ASP cc_start: 0.6746 (t0) cc_final: 0.6516 (t0) REVERT: D 216 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6853 (mm-30) REVERT: D 221 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: D 587 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6917 (mp0) REVERT: D 705 ASP cc_start: 0.7135 (t70) cc_final: 0.6878 (t0) REVERT: D 865 PHE cc_start: 0.8362 (m-80) cc_final: 0.7738 (t80) REVERT: D 962 ASP cc_start: 0.7043 (t0) cc_final: 0.6725 (t0) REVERT: D 965 THR cc_start: 0.8647 (t) cc_final: 0.8039 (t) REVERT: D 1003 LEU cc_start: 0.8458 (mt) cc_final: 0.7879 (mp) REVERT: D 1007 CYS cc_start: 0.7578 (p) cc_final: 0.7144 (p) REVERT: D 1059 ARG cc_start: 0.7277 (mtp85) cc_final: 0.7018 (mtp85) REVERT: D 1133 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7530 (pp) REVERT: D 1212 PHE cc_start: 0.8079 (t80) cc_final: 0.7779 (t80) REVERT: R 50 MET cc_start: 0.6840 (mtm) cc_final: 0.6623 (mtm) REVERT: S 32 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6646 (mt-10) REVERT: S 55 LEU cc_start: 0.8538 (tp) cc_final: 0.8269 (tt) REVERT: S 96 ASP cc_start: 0.5826 (OUTLIER) cc_final: 0.5577 (p0) outliers start: 41 outliers final: 32 residues processed: 426 average time/residue: 0.3268 time to fit residues: 202.5399 Evaluate side-chains 438 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 403 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 286 CYS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 403 LYS Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1093 LEU Chi-restraints excluded: chain D residue 1133 LEU Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 96 ASP Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 140 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 180 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 GLN D1140 GLN D1169 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18437 Z= 0.206 Angle : 0.507 11.427 24998 Z= 0.260 Chirality : 0.039 0.138 2984 Planarity : 0.004 0.048 3186 Dihedral : 3.469 19.964 2539 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.11 % Allowed : 16.07 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.18), residues: 2360 helix: 2.37 (0.13), residues: 1578 sheet: -0.89 (0.73), residues: 61 loop : -0.76 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 33 HIS 0.005 0.001 HIS D 707 PHE 0.020 0.001 PHE C 402 TYR 0.026 0.002 TYR C 50 ARG 0.003 0.000 ARG C 741 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 399 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 519 GLU cc_start: 0.7242 (tp30) cc_final: 0.6984 (tp30) REVERT: C 522 LYS cc_start: 0.7569 (tppp) cc_final: 0.7276 (tppt) REVERT: C 578 LYS cc_start: 0.8278 (ptmt) cc_final: 0.8038 (ptmm) REVERT: C 589 GLU cc_start: 0.6845 (mm-30) cc_final: 0.6271 (mm-30) REVERT: C 610 ILE cc_start: 0.8430 (pt) cc_final: 0.8145 (mt) REVERT: C 620 TYR cc_start: 0.6730 (m-80) cc_final: 0.6137 (m-80) REVERT: C 641 GLN cc_start: 0.7585 (tm-30) cc_final: 0.6740 (tm-30) REVERT: C 642 ILE cc_start: 0.8484 (mm) cc_final: 0.8128 (mm) REVERT: C 645 LYS cc_start: 0.7826 (mmtt) cc_final: 0.6866 (mmtt) REVERT: C 706 ASP cc_start: 0.7110 (m-30) cc_final: 0.6771 (m-30) REVERT: D 104 ASP cc_start: 0.7598 (p0) cc_final: 0.7205 (p0) REVERT: D 147 ASP cc_start: 0.6783 (t0) cc_final: 0.6565 (t0) REVERT: D 216 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6895 (mm-30) REVERT: D 221 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: D 705 ASP cc_start: 0.7145 (t70) cc_final: 0.6895 (t0) REVERT: D 962 ASP cc_start: 0.7054 (t0) cc_final: 0.6733 (t0) REVERT: D 965 THR cc_start: 0.8644 (t) cc_final: 0.8043 (t) REVERT: D 1003 LEU cc_start: 0.8471 (mt) cc_final: 0.7890 (mp) REVERT: D 1007 CYS cc_start: 0.7597 (p) cc_final: 0.7163 (p) REVERT: D 1059 ARG cc_start: 0.7281 (mtp85) cc_final: 0.7021 (mtp85) REVERT: D 1133 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7534 (pp) REVERT: D 1212 PHE cc_start: 0.8087 (t80) cc_final: 0.7782 (t80) REVERT: R 50 MET cc_start: 0.6841 (mtm) cc_final: 0.6619 (mtm) REVERT: S 14 PHE cc_start: 0.8112 (m-80) cc_final: 0.7672 (m-80) REVERT: S 32 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6649 (mt-10) REVERT: S 55 LEU cc_start: 0.8541 (tp) cc_final: 0.8255 (tt) REVERT: S 96 ASP cc_start: 0.5846 (OUTLIER) cc_final: 0.5578 (p0) REVERT: S 103 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7638 (tt) REVERT: S 105 LEU cc_start: 0.8108 (mm) cc_final: 0.7827 (mp) outliers start: 40 outliers final: 34 residues processed: 417 average time/residue: 0.3356 time to fit residues: 203.1124 Evaluate side-chains 436 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 398 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 503 LYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 638 GLN Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 286 CYS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 403 LYS Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1093 LEU Chi-restraints excluded: chain D residue 1133 LEU Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 96 ASP Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 140 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 0.8980 chunk 219 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 167 optimal weight: 0.0270 chunk 65 optimal weight: 0.6980 chunk 193 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 GLN D1140 GLN D1169 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18437 Z= 0.188 Angle : 0.505 16.426 24998 Z= 0.259 Chirality : 0.038 0.139 2984 Planarity : 0.004 0.048 3186 Dihedral : 3.459 21.678 2539 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.17 % Allowed : 16.33 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.18), residues: 2360 helix: 2.41 (0.13), residues: 1576 sheet: -0.84 (0.73), residues: 61 loop : -0.73 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 33 HIS 0.004 0.001 HIS D 707 PHE 0.020 0.001 PHE C 402 TYR 0.026 0.001 TYR C 50 ARG 0.003 0.000 ARG C 741 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 401 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 468 LYS cc_start: 0.8066 (mmmt) cc_final: 0.7865 (mtpp) REVERT: C 519 GLU cc_start: 0.7243 (tp30) cc_final: 0.6986 (tp30) REVERT: C 522 LYS cc_start: 0.7563 (tppp) cc_final: 0.7259 (tppt) REVERT: C 578 LYS cc_start: 0.8276 (ptmt) cc_final: 0.8033 (ptmm) REVERT: C 589 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6293 (mm-30) REVERT: C 610 ILE cc_start: 0.8425 (pt) cc_final: 0.8144 (mt) REVERT: C 620 TYR cc_start: 0.6669 (m-80) cc_final: 0.6087 (m-80) REVERT: C 633 MET cc_start: 0.7260 (mpp) cc_final: 0.7054 (mpp) REVERT: C 641 GLN cc_start: 0.7589 (tm-30) cc_final: 0.6753 (tm-30) REVERT: C 642 ILE cc_start: 0.8473 (mm) cc_final: 0.8111 (mm) REVERT: C 645 LYS cc_start: 0.7822 (mmtt) cc_final: 0.6885 (mmtt) REVERT: D 104 ASP cc_start: 0.7633 (p0) cc_final: 0.7227 (p0) REVERT: D 216 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6888 (mm-30) REVERT: D 221 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: D 587 GLU cc_start: 0.7098 (mp0) cc_final: 0.6864 (mp0) REVERT: D 705 ASP cc_start: 0.7150 (t70) cc_final: 0.6898 (t0) REVERT: D 902 GLN cc_start: 0.7815 (mt0) cc_final: 0.7596 (mt0) REVERT: D 962 ASP cc_start: 0.7049 (t0) cc_final: 0.6726 (t0) REVERT: D 1003 LEU cc_start: 0.8462 (mt) cc_final: 0.7877 (mp) REVERT: D 1007 CYS cc_start: 0.7577 (p) cc_final: 0.7141 (p) REVERT: D 1059 ARG cc_start: 0.7276 (mtp85) cc_final: 0.7018 (mtp85) REVERT: D 1133 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7552 (pp) REVERT: D 1212 PHE cc_start: 0.8083 (t80) cc_final: 0.7776 (t80) REVERT: R 50 MET cc_start: 0.6841 (mtm) cc_final: 0.6617 (mtm) REVERT: S 32 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6631 (mt-10) REVERT: S 55 LEU cc_start: 0.8547 (tp) cc_final: 0.8265 (tt) REVERT: S 96 ASP cc_start: 0.5806 (OUTLIER) cc_final: 0.5540 (p0) REVERT: S 103 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7635 (tt) outliers start: 41 outliers final: 35 residues processed: 419 average time/residue: 0.3509 time to fit residues: 215.5455 Evaluate side-chains 436 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 397 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 638 GLN Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 286 CYS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 403 LYS Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 738 LEU Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1093 LEU Chi-restraints excluded: chain D residue 1133 LEU Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 96 ASP Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 157 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 50.0000 chunk 137 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 237 optimal weight: 10.0000 chunk 218 optimal weight: 30.0000 chunk 188 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 GLN D1140 GLN D1169 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18437 Z= 0.219 Angle : 0.518 13.166 24998 Z= 0.266 Chirality : 0.039 0.188 2984 Planarity : 0.004 0.048 3186 Dihedral : 3.491 23.228 2539 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.11 % Allowed : 16.54 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.18), residues: 2360 helix: 2.35 (0.13), residues: 1578 sheet: -1.25 (0.67), residues: 71 loop : -0.68 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 33 HIS 0.005 0.001 HIS D 707 PHE 0.021 0.001 PHE C 402 TYR 0.027 0.002 TYR C 50 ARG 0.004 0.000 ARG D1144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 404 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 298 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7472 (mtpt) REVERT: C 519 GLU cc_start: 0.7243 (tp30) cc_final: 0.6988 (tp30) REVERT: C 522 LYS cc_start: 0.7583 (tppp) cc_final: 0.7280 (tppt) REVERT: C 589 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6291 (mm-30) REVERT: C 610 ILE cc_start: 0.8435 (pt) cc_final: 0.8158 (mt) REVERT: C 620 TYR cc_start: 0.6690 (m-80) cc_final: 0.6086 (m-80) REVERT: C 641 GLN cc_start: 0.7595 (tm-30) cc_final: 0.6744 (tm-30) REVERT: C 642 ILE cc_start: 0.8479 (mm) cc_final: 0.8117 (mm) REVERT: C 645 LYS cc_start: 0.7846 (mmtt) cc_final: 0.6897 (mmtt) REVERT: C 706 ASP cc_start: 0.6985 (m-30) cc_final: 0.6723 (m-30) REVERT: D 104 ASP cc_start: 0.7610 (p0) cc_final: 0.7202 (p0) REVERT: D 216 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6891 (mm-30) REVERT: D 221 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: D 587 GLU cc_start: 0.7112 (mp0) cc_final: 0.6783 (mp0) REVERT: D 705 ASP cc_start: 0.7163 (t70) cc_final: 0.6899 (t0) REVERT: D 902 GLN cc_start: 0.7831 (mt0) cc_final: 0.7624 (mt0) REVERT: D 962 ASP cc_start: 0.7115 (t0) cc_final: 0.6880 (t0) REVERT: D 1003 LEU cc_start: 0.8477 (mt) cc_final: 0.7893 (mp) REVERT: D 1007 CYS cc_start: 0.7597 (p) cc_final: 0.7166 (p) REVERT: D 1059 ARG cc_start: 0.7288 (mtp85) cc_final: 0.7026 (mtp85) REVERT: D 1133 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7529 (pp) REVERT: D 1178 ARG cc_start: 0.8046 (ttm170) cc_final: 0.7719 (mtm-85) REVERT: D 1212 PHE cc_start: 0.8087 (t80) cc_final: 0.7764 (t80) REVERT: R 50 MET cc_start: 0.6846 (mtm) cc_final: 0.6616 (mtm) REVERT: S 32 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6636 (mt-10) REVERT: S 55 LEU cc_start: 0.8555 (tp) cc_final: 0.8269 (tt) REVERT: S 96 ASP cc_start: 0.5835 (OUTLIER) cc_final: 0.5579 (p0) REVERT: S 103 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7629 (tt) REVERT: S 105 LEU cc_start: 0.8138 (mm) cc_final: 0.7857 (mp) outliers start: 40 outliers final: 34 residues processed: 423 average time/residue: 0.3298 time to fit residues: 202.9668 Evaluate side-chains 440 residues out of total 2163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 401 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 638 GLN Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 286 CYS Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 403 LYS Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 738 LEU Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1093 LEU Chi-restraints excluded: chain D residue 1133 LEU Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain D residue 1215 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 96 ASP Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 157 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 189 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 GLN D1140 GLN D1169 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.130664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.104817 restraints weight = 25891.472| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.86 r_work: 0.3148 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 18437 Z= 0.286 Angle : 0.555 13.270 24998 Z= 0.285 Chirality : 0.041 0.172 2984 Planarity : 0.004 0.048 3186 Dihedral : 3.629 23.634 2539 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.17 % Allowed : 16.60 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.18), residues: 2360 helix: 2.26 (0.13), residues: 1574 sheet: -1.31 (0.66), residues: 71 loop : -0.69 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 127 HIS 0.007 0.001 HIS D 707 PHE 0.023 0.002 PHE C 402 TYR 0.027 0.002 TYR C 50 ARG 0.005 0.000 ARG D1141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5006.93 seconds wall clock time: 90 minutes 7.04 seconds (5407.04 seconds total)