Starting phenix.real_space_refine on Wed Feb 14 22:47:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p92_13258/02_2024/7p92_13258_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p92_13258/02_2024/7p92_13258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p92_13258/02_2024/7p92_13258.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p92_13258/02_2024/7p92_13258.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p92_13258/02_2024/7p92_13258_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p92_13258/02_2024/7p92_13258_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 34 7.16 5 Zn 1 6.06 5 P 1 5.49 5 S 114 5.16 5 C 6472 2.51 5 N 1730 2.21 5 O 2084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 86": "OE1" <-> "OE2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10436 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4376 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 554, 4365 Classifications: {'peptide': 554} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 532} Conformer: "B" Number of residues, atoms: 554, 4365 Classifications: {'peptide': 554} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 532} bond proxies already assigned to first conformer: 4425 Chain: "B" Number of atoms: 4585 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 612, 4577 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 580} Chain breaks: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 62 Conformer: "B" Number of residues, atoms: 612, 4577 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 580} Chain breaks: 1 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 62 bond proxies already assigned to first conformer: 4653 Chain: "C" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1218 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 148} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {'FES': 1, 'SF4': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 60 Unusual residues: {' ZN': 1, 'FES': 1, 'FMN': 1, 'SF4': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 132 Classifications: {'water': 132} Link IDs: {None: 131} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2758 SG CYS A 350 76.094 68.056 75.135 1.00 7.59 S ATOM 2316 SG CYS A 295 70.402 70.632 76.629 1.00 15.55 S ATOM 3806 SG CYS A 486 74.752 69.368 81.232 1.00 15.55 S ATOM 3776 SG CYS A 482 71.757 64.495 77.601 1.00 8.52 S ATOM 1222 SG CYS A 153 65.862 60.075 68.302 1.00 15.55 S ATOM 1515 SG CYS A 192 71.900 58.207 69.319 1.00 15.55 S ATOM 1496 SG CYS A 189 69.750 62.975 72.476 1.00 15.55 S ATOM 1475 SG CYS A 186 70.872 63.816 66.223 1.00 15.55 S ATOM 1545 SG CYS A 196 74.895 51.015 69.541 1.00 15.55 S ATOM 1191 SG CYS A 149 69.171 52.733 67.459 1.00 15.55 S ATOM 1173 SG CYS A 146 70.040 47.258 70.514 1.00 15.55 S ATOM 1151 SG CYS A 143 71.821 47.899 64.339 1.00 15.55 S ATOM 825 SG CYS A 105 80.344 44.271 71.706 1.00 15.55 S ATOM 762 SG CYS A 96 85.941 42.905 68.371 1.00 15.55 S ATOM 782 SG CYS A 99 83.223 48.709 68.392 1.00 15.55 S ATOM 377 SG CYS A 48 65.096 33.681 75.979 1.00 7.95 S ATOM 464 SG CYS A 60 62.624 36.306 75.858 1.00 9.17 S ATOM 271 SG CYS A 34 66.250 39.621 73.336 1.00 7.94 S ATOM 352 SG CYS A 45 68.443 36.750 72.900 1.00 15.55 S ATOM 8774 SG CYS B 588 87.917 28.834 25.382 1.00 47.57 S ATOM 8877 SG CYS B 608 84.009 25.515 29.155 1.00 51.02 S ATOM 8908 SG CYS B 614 81.727 27.263 23.766 1.00 52.63 S ATOM 8893 SG CYS B 611 83.209 31.619 28.640 1.00 52.63 S ATOM 8738 SG CYS B 581 84.135 29.198 11.632 1.00 57.57 S ATOM 8753 SG CYS B 584 86.565 26.230 16.586 1.00 54.61 S ATOM 8723 SG CYS B 578 81.923 23.294 13.234 1.00 48.09 S ATOM 8929 SG CYS B 618 80.658 28.677 16.893 1.00 51.77 S ATOM 8030 SG CYS B 485 59.775 40.451 61.575 1.00 8.10 S ATOM 8069 SG CYS B 491 62.595 34.858 59.436 1.00 9.22 S ATOM 8388 SG CYS B 531 56.796 35.119 62.533 1.00 15.46 S ATOM 8049 SG CYS B 488 63.213 35.635 64.600 1.00 15.55 S ATOM 4632 SG CYS B 31 35.161 32.924 35.511 1.00 33.27 S ATOM 4660 SG CYS B 36 37.749 32.402 33.129 1.00 30.10 S ATOM 4895 SG CYS B 78 37.178 29.852 39.546 1.00 33.00 S ATOM 4922 SG CYS B 82 40.030 29.454 37.554 1.00 32.46 S ATOM 7886 SG CYS B 468 67.438 20.304 41.306 1.00 22.67 S ATOM 8612 SG CYS B 560 69.489 19.038 38.306 1.00 27.99 S ATOM 8643 SG CYS B 565 69.963 22.604 39.651 1.00 31.40 S ATOM 9876 SG CYS C 119 48.824 32.667 41.485 1.00 19.72 S ATOM 9899 SG CYS C 123 48.616 29.924 39.489 1.00 21.32 S ATOM 9582 SG CYS C 78 53.316 34.474 39.243 1.00 19.40 S ATOM 9612 SG CYS C 83 53.317 32.227 36.513 1.00 17.79 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 130 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 130 " occ=0.50 Time building chain proxies: 9.93, per 1000 atoms: 0.95 Number of scatterers: 10436 At special positions: 0 Unit cell: (112.888, 106.296, 110.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 34 26.01 S 114 16.00 P 1 15.00 O 2084 8.00 N 1730 7.00 C 6472 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: 4.65 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 705 " pdb="FE1 FES A 705 " - pdb=" SG CYS A 48 " pdb="FE2 FES A 705 " - pdb=" SG CYS A 34 " pdb="FE2 FES A 705 " - pdb=" SG CYS A 45 " pdb="FE1 FES A 705 " - pdb=" SG CYS A 60 " pdb=" FES B 704 " pdb="FE2 FES B 704 " - pdb=" SG CYS B 82 " pdb="FE1 FES B 704 " - pdb=" SG CYS B 31 " pdb="FE1 FES B 704 " - pdb=" SG CYS B 36 " pdb="FE2 FES B 704 " - pdb=" SG CYS B 78 " pdb=" FES C 201 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 78 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 83 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 123 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 119 " pdb=" SF4 A 701 " pdb="FE4 SF4 A 701 " - pdb=" SG CYS A 482 " pdb="FE1 SF4 A 701 " - pdb=" SG CYS A 350 " pdb="FE2 SF4 A 701 " - pdb=" SG CYS A 295 " pdb="FE3 SF4 A 701 " - pdb=" SG CYS A 486 " pdb=" SF4 A 702 " pdb="FE4 SF4 A 702 " - pdb=" SG CYS A 186 " pdb="FE2 SF4 A 702 " - pdb=" SG CYS A 192 " pdb="FE1 SF4 A 702 " - pdb=" SG CYS A 153 " pdb="FE3 SF4 A 702 " - pdb=" SG CYS A 189 " pdb=" SF4 A 703 " pdb="FE3 SF4 A 703 " - pdb=" SG CYS A 146 " pdb="FE2 SF4 A 703 " - pdb=" SG CYS A 149 " pdb="FE4 SF4 A 703 " - pdb=" SG CYS A 143 " pdb="FE1 SF4 A 703 " - pdb=" SG CYS A 196 " pdb=" SF4 A 704 " pdb="FE2 SF4 A 704 " - pdb=" NE2 HIS A 92 " pdb="FE4 SF4 A 704 " - pdb=" SG CYS A 99 " pdb="FE3 SF4 A 704 " - pdb=" SG CYS A 96 " pdb="FE1 SF4 A 704 " - pdb=" SG CYS A 105 " pdb=" SF4 B 700 " pdb="FE1 SF4 B 700 " - pdb=" SG CYS B 588 " pdb="FE4 SF4 B 700 " - pdb=" SG CYS B 611 " pdb="FE2 SF4 B 700 " - pdb=" SG CYS B 608 " pdb="FE3 SF4 B 700 " - pdb=" SG CYS B 614 " pdb=" SF4 B 701 " pdb="FE1 SF4 B 701 " - pdb=" SG CYS B 581 " pdb="FE4 SF4 B 701 " - pdb=" SG CYS B 618 " pdb="FE2 SF4 B 701 " - pdb=" SG CYS B 584 " pdb="FE3 SF4 B 701 " - pdb=" SG CYS B 578 " pdb=" SF4 B 702 " pdb="FE1 SF4 B 702 " - pdb=" SG CYS B 485 " pdb="FE3 SF4 B 702 " - pdb=" SG CYS B 531 " pdb="FE4 SF4 B 702 " - pdb=" SG CYS B 488 " pdb="FE2 SF4 B 702 " - pdb=" SG CYS B 491 " Number of angles added : 99 Zn2+ tetrahedral coordination pdb=" ZN B 705 " pdb="ZN ZN B 705 " - pdb=" NE2 HIS B 555 " pdb="ZN ZN B 705 " - pdb=" SG CYS B 565 " pdb="ZN ZN B 705 " - pdb=" SG CYS B 468 " pdb="ZN ZN B 705 " - pdb=" SG CYS B 560 " Number of angles added : 3 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2418 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 10 sheets defined 42.7% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 75 through 90 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 148 through 155 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 244 through 254 Processing helix chain 'A' and resid 263 through 284 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 319 through 329 Processing helix chain 'A' and resid 331 through 334 No H-bonds generated for 'chain 'A' and resid 331 through 334' Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 352 through 358 removed outlier: 3.594A pdb=" N GLU A 358 " --> pdb=" O LYS A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 382 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 403 through 409 removed outlier: 3.563A pdb=" N PHE A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLY A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 425 Processing helix chain 'A' and resid 463 through 469 Processing helix chain 'A' and resid 485 through 488 Processing helix chain 'A' and resid 498 through 513 Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 524 through 533 Processing helix chain 'A' and resid 537 through 544 Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 41 through 55 Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 161 through 166 Processing helix chain 'B' and resid 171 through 178 Processing helix chain 'B' and resid 182 through 191 Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 243 through 256 Processing helix chain 'B' and resid 271 through 286 Processing helix chain 'B' and resid 312 through 315 Processing helix chain 'B' and resid 317 through 324 Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 353 through 364 removed outlier: 3.604A pdb=" N ILE B 359 " --> pdb=" O THR B 355 " (cutoff:3.500A) Proline residue: B 360 - end of helix Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 428 through 430 No H-bonds generated for 'chain 'B' and resid 428 through 430' Processing helix chain 'B' and resid 445 through 449 removed outlier: 3.547A pdb=" N LYS B 449 " --> pdb=" O TYR B 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 445 through 449' Processing helix chain 'B' and resid 469 through 483 Processing helix chain 'B' and resid 489 through 507 removed outlier: 4.105A pdb=" N MET B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 528 Processing helix chain 'B' and resid 532 through 535 No H-bonds generated for 'chain 'B' and resid 532 through 535' Processing helix chain 'B' and resid 537 through 557 Proline residue: B 540 - end of helix removed outlier: 3.914A pdb=" N PHE B 548 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ARG B 549 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLU B 550 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 577 No H-bonds generated for 'chain 'B' and resid 575 through 577' Processing helix chain 'C' and resid 6 through 15 Processing helix chain 'C' and resid 19 through 33 removed outlier: 5.418A pdb=" N ILE C 23 " --> pdb=" O GLU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 48 Processing helix chain 'C' and resid 52 through 61 Processing helix chain 'C' and resid 81 through 86 Processing helix chain 'C' and resid 88 through 99 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 141 through 158 removed outlier: 3.702A pdb=" N SER C 158 " --> pdb=" O LYS C 154 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 2 through 5 Processing sheet with id= B, first strand: chain 'A' and resid 49 through 52 Processing sheet with id= C, first strand: chain 'A' and resid 136 through 138 Processing sheet with id= D, first strand: chain 'A' and resid 163 through 165 Processing sheet with id= E, first strand: chain 'A' and resid 259 through 262 removed outlier: 3.561A pdb=" N LYS A 259 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE A 368 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N MET A 348 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU A 370 " --> pdb=" O MET A 348 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 476 through 480 removed outlier: 3.943A pdb=" N LYS A 430 " --> pdb=" O THR A 446 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 72 through 76 Processing sheet with id= H, first strand: chain 'B' and resid 348 through 352 removed outlier: 6.727A pdb=" N PHE B 220 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ASN B 351 " --> pdb=" O PHE B 220 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 222 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS B 261 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N CYS B 223 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR B 263 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASP B 302 " --> pdb=" O GLY B 262 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ALA B 264 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU B 304 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE B 266 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LYS B 306 " --> pdb=" O ILE B 266 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 394 through 399 Processing sheet with id= J, first strand: chain 'C' and resid 112 through 117 removed outlier: 6.713A pdb=" N TYR C 73 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ASP C 115 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE C 75 " --> pdb=" O ASP C 115 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL C 117 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL C 77 " --> pdb=" O VAL C 117 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 1002 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: 3.35 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 4102 1.40 - 1.62: 6180 1.62 - 1.84: 110 1.84 - 2.06: 0 2.06 - 2.28: 96 Bond restraints: 10488 Sorted by residual: bond pdb=" C ARG C 149 " pdb=" O ARG C 149 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.15e-02 7.56e+03 2.36e+01 bond pdb=" N ARG C 34 " pdb=" CA ARG C 34 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.77e+00 bond pdb=" CA ARG C 149 " pdb=" C ARG C 149 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.24e-02 6.50e+03 5.28e+00 bond pdb=" C GLU C 153 " pdb=" O GLU C 153 " ideal model delta sigma weight residual 1.237 1.215 0.021 1.16e-02 7.43e+03 3.37e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 ... (remaining 10483 not shown) Histogram of bond angle deviations from ideal: 73.53 - 85.62: 90 85.62 - 97.71: 0 97.71 - 109.80: 1244 109.80 - 121.88: 10778 121.88 - 133.97: 2089 Bond angle restraints: 14201 Sorted by residual: angle pdb=" N ARG C 149 " pdb=" CA ARG C 149 " pdb=" C ARG C 149 " ideal model delta sigma weight residual 110.97 107.52 3.45 1.09e+00 8.42e-01 1.00e+01 angle pdb=" CA ARG C 149 " pdb=" C ARG C 149 " pdb=" O ARG C 149 " ideal model delta sigma weight residual 121.00 117.98 3.02 1.05e+00 9.07e-01 8.30e+00 angle pdb=" N ARG C 34 " pdb=" CA ARG C 34 " pdb=" CB ARG C 34 " ideal model delta sigma weight residual 110.49 115.25 -4.76 1.69e+00 3.50e-01 7.93e+00 angle pdb=" CA ARG C 149 " pdb=" C ARG C 149 " pdb=" N LYS C 150 " ideal model delta sigma weight residual 116.92 120.07 -3.15 1.16e+00 7.43e-01 7.37e+00 angle pdb=" N GLN B 10 " pdb=" CA GLN B 10 " pdb=" CB GLN B 10 " ideal model delta sigma weight residual 110.12 113.88 -3.76 1.47e+00 4.63e-01 6.56e+00 ... (remaining 14196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.79: 6230 34.79 - 69.59: 110 69.59 - 104.38: 11 104.38 - 139.18: 0 139.18 - 173.97: 1 Dihedral angle restraints: 6352 sinusoidal: 2565 harmonic: 3787 Sorted by residual: dihedral pdb=" C10 FMN B 703 " pdb=" C1' FMN B 703 " pdb=" N10 FMN B 703 " pdb=" C2' FMN B 703 " ideal model delta sinusoidal sigma weight residual 257.59 83.62 173.97 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" N ARG C 34 " pdb=" C ARG C 34 " pdb=" CA ARG C 34 " pdb=" CB ARG C 34 " ideal model delta harmonic sigma weight residual 122.80 133.11 -10.31 0 2.50e+00 1.60e-01 1.70e+01 dihedral pdb=" C ARG C 34 " pdb=" N ARG C 34 " pdb=" CA ARG C 34 " pdb=" CB ARG C 34 " ideal model delta harmonic sigma weight residual -122.60 -131.76 9.16 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 6349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1390 0.063 - 0.126: 205 0.126 - 0.189: 5 0.189 - 0.251: 0 0.251 - 0.314: 1 Chirality restraints: 1601 Sorted by residual: chirality pdb=" CA ARG C 34 " pdb=" N ARG C 34 " pdb=" C ARG C 34 " pdb=" CB ARG C 34 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA ILE B 90 " pdb=" N ILE B 90 " pdb=" C ILE B 90 " pdb=" CB ILE B 90 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA GLU A 374 " pdb=" N GLU A 374 " pdb=" C GLU A 374 " pdb=" CB GLU A 374 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 1598 not shown) Planarity restraints: 1810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 334 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.90e+00 pdb=" N PRO B 335 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 335 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 335 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 101 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.71e+00 pdb=" N PRO B 102 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 102 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 102 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 491 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C CYS B 491 " -0.027 2.00e-02 2.50e+03 pdb=" O CYS B 491 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG B 492 " 0.009 2.00e-02 2.50e+03 ... (remaining 1807 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 107 2.57 - 3.15: 8740 3.15 - 3.73: 16927 3.73 - 4.32: 24493 4.32 - 4.90: 39454 Nonbonded interactions: 89721 Sorted by model distance: nonbonded pdb=" O HOH A 885 " pdb=" O HOH A 910 " model vdw 1.985 2.440 nonbonded pdb=" O HOH A 907 " pdb=" O HOH A 917 " model vdw 1.995 2.440 nonbonded pdb=" O PHE A 169 " pdb=" O HOH A 801 " model vdw 1.999 2.440 nonbonded pdb=" O PHE B 475 " pdb=" O HOH B 801 " model vdw 2.005 2.440 nonbonded pdb=" O HOH A 889 " pdb=" O HOH A 890 " model vdw 2.020 2.440 ... (remaining 89716 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 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: 0.010 Extract box with map and model: 7.730 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 41.860 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 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:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 0.056 10488 Z= 0.216 Angle : 0.564 6.256 14201 Z= 0.311 Chirality : 0.043 0.314 1601 Planarity : 0.004 0.046 1810 Dihedral : 14.117 173.970 3934 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.18 % Allowed : 0.18 % Favored : 99.63 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.23), residues: 1318 helix: 1.30 (0.22), residues: 575 sheet: -0.91 (0.43), residues: 124 loop : -0.67 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 344 HIS 0.004 0.001 HIS A 276 PHE 0.011 0.001 PHE B 123 TYR 0.019 0.001 TYR A 459 ARG 0.004 0.001 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 1.293 Fit side-chains revert: symmetry clash REVERT: A 432 ASP cc_start: 0.6630 (m-30) cc_final: 0.6305 (m-30) REVERT: A 435 SER cc_start: 0.8023 (m) cc_final: 0.7802 (p) REVERT: A 506 LYS cc_start: 0.7970 (ttpp) cc_final: 0.7758 (ttpp) REVERT: B 276 MET cc_start: 0.7644 (mmp) cc_final: 0.7427 (mmp) REVERT: C 105 ASN cc_start: 0.7653 (m-40) cc_final: 0.7342 (m-40) REVERT: C 111 MET cc_start: 0.6345 (tpp) cc_final: 0.6143 (tpp) outliers start: 1 outliers final: 0 residues processed: 196 average time/residue: 1.6072 time to fit residues: 333.9200 Evaluate side-chains 167 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 55 GLN B 4 ASN C 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10488 Z= 0.283 Angle : 0.614 17.089 14201 Z= 0.313 Chirality : 0.046 0.173 1601 Planarity : 0.005 0.061 1810 Dihedral : 6.583 171.969 1455 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.49 % Allowed : 8.10 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.23), residues: 1318 helix: 1.02 (0.22), residues: 580 sheet: -0.74 (0.43), residues: 130 loop : -0.61 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 344 HIS 0.004 0.001 HIS A 92 PHE 0.016 0.002 PHE B 301 TYR 0.016 0.002 TYR A 459 ARG 0.006 0.001 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 1.356 Fit side-chains REVERT: A 120 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6964 (ttm-80) REVERT: A 432 ASP cc_start: 0.6623 (m-30) cc_final: 0.6262 (m-30) REVERT: B 276 MET cc_start: 0.7644 (mmp) cc_final: 0.7429 (mmp) REVERT: C 19 ARG cc_start: 0.6323 (tmt-80) cc_final: 0.6085 (tmt-80) REVERT: C 72 LYS cc_start: 0.6364 (OUTLIER) cc_final: 0.5847 (ttmt) REVERT: C 105 ASN cc_start: 0.7690 (m-40) cc_final: 0.7295 (m-40) outliers start: 26 outliers final: 7 residues processed: 174 average time/residue: 1.6092 time to fit residues: 297.0251 Evaluate side-chains 164 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 155 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 155 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 55 GLN B 4 ASN B 260 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10488 Z= 0.174 Angle : 0.524 17.198 14201 Z= 0.264 Chirality : 0.042 0.166 1601 Planarity : 0.005 0.047 1810 Dihedral : 6.347 171.291 1455 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.47 % Allowed : 11.60 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.23), residues: 1318 helix: 1.30 (0.22), residues: 575 sheet: -0.83 (0.42), residues: 136 loop : -0.56 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 208 HIS 0.002 0.001 HIS B 520 PHE 0.011 0.001 PHE A 394 TYR 0.012 0.001 TYR A 459 ARG 0.007 0.000 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 160 time to evaluate : 1.241 Fit side-chains REVERT: A 388 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6844 (mtt-85) REVERT: A 432 ASP cc_start: 0.6558 (m-30) cc_final: 0.6176 (m-30) REVERT: A 480 MET cc_start: 0.8329 (mmm) cc_final: 0.7881 (mmt) REVERT: B 48 PHE cc_start: 0.7051 (OUTLIER) cc_final: 0.6352 (m-10) REVERT: B 276 MET cc_start: 0.7627 (mmp) cc_final: 0.7418 (mmp) REVERT: C 19 ARG cc_start: 0.6297 (tmt-80) cc_final: 0.6061 (tmt-80) outliers start: 15 outliers final: 8 residues processed: 166 average time/residue: 1.5360 time to fit residues: 271.2670 Evaluate side-chains 163 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 461 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN B 4 ASN B 260 GLN C 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10488 Z= 0.377 Angle : 0.667 19.201 14201 Z= 0.340 Chirality : 0.048 0.195 1601 Planarity : 0.006 0.067 1810 Dihedral : 6.809 171.268 1455 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.95 % Allowed : 12.43 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.23), residues: 1318 helix: 0.88 (0.22), residues: 575 sheet: -0.76 (0.43), residues: 130 loop : -0.77 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.003 TRP B 344 HIS 0.006 0.002 HIS B 520 PHE 0.019 0.002 PHE B 301 TYR 0.014 0.002 TYR A 459 ARG 0.005 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 155 time to evaluate : 1.246 Fit side-chains REVERT: A 274 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7416 (tp30) REVERT: A 388 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6844 (mtt-85) REVERT: A 425 GLU cc_start: 0.6378 (tt0) cc_final: 0.6053 (mp0) REVERT: A 432 ASP cc_start: 0.6589 (m-30) cc_final: 0.6149 (m-30) REVERT: A 480 MET cc_start: 0.8324 (mmm) cc_final: 0.8070 (mmt) REVERT: B 398 VAL cc_start: 0.7823 (m) cc_final: 0.7469 (p) REVERT: C 72 LYS cc_start: 0.6268 (OUTLIER) cc_final: 0.5815 (ttmt) REVERT: C 134 GLU cc_start: 0.5684 (tp30) cc_final: 0.5396 (mm-30) outliers start: 31 outliers final: 14 residues processed: 171 average time/residue: 1.6072 time to fit residues: 291.6366 Evaluate side-chains 166 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 155 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 87 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 ASN B 260 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10488 Z= 0.192 Angle : 0.546 18.519 14201 Z= 0.273 Chirality : 0.043 0.163 1601 Planarity : 0.005 0.049 1810 Dihedral : 6.495 171.027 1455 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.66 % Allowed : 14.46 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.23), residues: 1318 helix: 1.16 (0.22), residues: 574 sheet: -0.69 (0.43), residues: 130 loop : -0.66 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 208 HIS 0.003 0.001 HIS B 520 PHE 0.011 0.001 PHE A 394 TYR 0.011 0.001 TYR A 272 ARG 0.007 0.000 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 1.211 Fit side-chains REVERT: A 388 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6823 (mtt-85) REVERT: A 432 ASP cc_start: 0.6510 (m-30) cc_final: 0.6077 (m-30) REVERT: A 480 MET cc_start: 0.8218 (mmm) cc_final: 0.7933 (mmt) REVERT: B 48 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.5882 (t80) REVERT: C 72 LYS cc_start: 0.6276 (OUTLIER) cc_final: 0.5981 (ptmt) REVERT: C 134 GLU cc_start: 0.5680 (tp30) cc_final: 0.5382 (mm-30) outliers start: 18 outliers final: 10 residues processed: 167 average time/residue: 1.5956 time to fit residues: 283.1989 Evaluate side-chains 164 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 155 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.7980 chunk 114 optimal weight: 9.9990 chunk 25 optimal weight: 0.0000 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN B 4 ASN B 260 GLN C 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10488 Z= 0.172 Angle : 0.523 17.425 14201 Z= 0.261 Chirality : 0.042 0.153 1601 Planarity : 0.005 0.049 1810 Dihedral : 6.332 170.418 1455 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.12 % Allowed : 14.36 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.23), residues: 1318 helix: 1.30 (0.22), residues: 577 sheet: -0.57 (0.44), residues: 130 loop : -0.56 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 208 HIS 0.002 0.001 HIS B 520 PHE 0.011 0.001 PHE A 394 TYR 0.011 0.001 TYR A 65 ARG 0.009 0.000 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 157 time to evaluate : 1.177 Fit side-chains REVERT: A 388 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6823 (mtt-85) REVERT: A 432 ASP cc_start: 0.6507 (m-30) cc_final: 0.6066 (m-30) REVERT: A 466 LYS cc_start: 0.7635 (tttm) cc_final: 0.7092 (pttp) REVERT: A 480 MET cc_start: 0.8165 (mmm) cc_final: 0.7858 (mmt) REVERT: B 48 PHE cc_start: 0.6962 (OUTLIER) cc_final: 0.5898 (t80) REVERT: B 209 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6808 (mm-30) REVERT: B 283 ASP cc_start: 0.5888 (m-30) cc_final: 0.5680 (m-30) REVERT: C 134 GLU cc_start: 0.5587 (tp30) cc_final: 0.5230 (mm-30) outliers start: 23 outliers final: 9 residues processed: 168 average time/residue: 1.5361 time to fit residues: 274.8508 Evaluate side-chains 163 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 151 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 155 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN B 4 ASN B 99 ASN B 260 GLN C 116 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10488 Z= 0.230 Angle : 0.561 17.761 14201 Z= 0.282 Chirality : 0.044 0.166 1601 Planarity : 0.005 0.055 1810 Dihedral : 6.498 170.594 1455 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.49 % Allowed : 14.27 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.23), residues: 1318 helix: 1.21 (0.22), residues: 575 sheet: -0.57 (0.44), residues: 130 loop : -0.59 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.002 TRP B 344 HIS 0.004 0.001 HIS B 520 PHE 0.010 0.002 PHE A 467 TYR 0.010 0.001 TYR A 65 ARG 0.010 0.001 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 1.347 Fit side-chains REVERT: A 388 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6818 (mtt-85) REVERT: A 432 ASP cc_start: 0.6466 (m-30) cc_final: 0.6046 (m-30) REVERT: A 466 LYS cc_start: 0.7629 (tttm) cc_final: 0.7074 (pttp) REVERT: A 480 MET cc_start: 0.8195 (mmm) cc_final: 0.7978 (mmt) REVERT: B 48 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.5894 (t80) REVERT: B 209 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6838 (mm-30) REVERT: B 398 VAL cc_start: 0.7846 (m) cc_final: 0.7468 (p) REVERT: C 134 GLU cc_start: 0.5581 (tp30) cc_final: 0.5245 (mm-30) outliers start: 27 outliers final: 13 residues processed: 161 average time/residue: 1.4419 time to fit residues: 247.9381 Evaluate side-chains 164 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 155 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 0.4980 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 ASN B 99 ASN B 260 GLN C 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10488 Z= 0.217 Angle : 0.553 17.936 14201 Z= 0.277 Chirality : 0.043 0.168 1601 Planarity : 0.005 0.052 1810 Dihedral : 6.478 170.636 1455 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.66 % Allowed : 15.29 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.23), residues: 1318 helix: 1.19 (0.22), residues: 576 sheet: -0.56 (0.44), residues: 130 loop : -0.56 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 208 HIS 0.004 0.001 HIS B 520 PHE 0.010 0.002 PHE A 467 TYR 0.010 0.001 TYR A 65 ARG 0.011 0.001 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 149 time to evaluate : 1.260 Fit side-chains REVERT: A 118 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7197 (pmtt) REVERT: A 374 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7186 (mt-10) REVERT: A 388 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6818 (mtt-85) REVERT: A 432 ASP cc_start: 0.6434 (m-30) cc_final: 0.6004 (m-30) REVERT: A 466 LYS cc_start: 0.7641 (tttm) cc_final: 0.7078 (pttp) REVERT: A 480 MET cc_start: 0.8175 (mmm) cc_final: 0.7928 (mmt) REVERT: B 48 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.5885 (t80) REVERT: B 398 VAL cc_start: 0.7854 (m) cc_final: 0.7474 (p) REVERT: C 134 GLU cc_start: 0.5539 (tp30) cc_final: 0.5202 (mm-30) outliers start: 18 outliers final: 13 residues processed: 158 average time/residue: 1.4538 time to fit residues: 245.3206 Evaluate side-chains 164 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 155 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.0020 chunk 110 optimal weight: 7.9990 chunk 117 optimal weight: 0.7980 chunk 70 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 overall best weight: 1.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 ASN B 99 ASN B 260 GLN C 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10488 Z= 0.274 Angle : 0.598 18.830 14201 Z= 0.301 Chirality : 0.045 0.179 1601 Planarity : 0.005 0.060 1810 Dihedral : 6.658 170.757 1455 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.03 % Allowed : 15.10 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.23), residues: 1318 helix: 1.06 (0.22), residues: 575 sheet: -0.65 (0.44), residues: 130 loop : -0.62 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP B 344 HIS 0.005 0.001 HIS B 520 PHE 0.011 0.002 PHE A 467 TYR 0.011 0.002 TYR A 65 ARG 0.011 0.001 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 1.312 Fit side-chains REVERT: A 118 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7224 (pmtt) REVERT: A 374 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7144 (mt-10) REVERT: A 388 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6830 (mtt-85) REVERT: A 432 ASP cc_start: 0.6447 (m-30) cc_final: 0.6020 (m-30) REVERT: B 48 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.5849 (t80) REVERT: B 207 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.6047 (mtmt) REVERT: B 398 VAL cc_start: 0.7851 (m) cc_final: 0.7485 (p) REVERT: C 134 GLU cc_start: 0.5561 (tp30) cc_final: 0.5224 (mm-30) outliers start: 22 outliers final: 13 residues processed: 158 average time/residue: 1.5585 time to fit residues: 262.6054 Evaluate side-chains 164 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 207 LYS Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 155 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 86 optimal weight: 0.0020 chunk 130 optimal weight: 0.9980 chunk 120 optimal weight: 0.1980 chunk 103 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 110 optimal weight: 8.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 ASN B 99 ASN B 260 GLN C 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10488 Z= 0.151 Angle : 0.515 17.563 14201 Z= 0.255 Chirality : 0.042 0.154 1601 Planarity : 0.005 0.055 1810 Dihedral : 6.315 170.487 1455 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.47 % Allowed : 15.56 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.24), residues: 1318 helix: 1.32 (0.22), residues: 576 sheet: -0.41 (0.44), residues: 128 loop : -0.47 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 208 HIS 0.003 0.001 HIS B 555 PHE 0.012 0.001 PHE A 394 TYR 0.011 0.001 TYR A 272 ARG 0.013 0.000 ARG C 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 1.358 Fit side-chains REVERT: A 118 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.7228 (pmtt) REVERT: A 432 ASP cc_start: 0.6419 (m-30) cc_final: 0.5988 (m-30) REVERT: A 466 LYS cc_start: 0.7618 (tttm) cc_final: 0.7032 (pttp) REVERT: B 1 MET cc_start: 0.3600 (pmm) cc_final: 0.2539 (ptp) REVERT: B 48 PHE cc_start: 0.6954 (OUTLIER) cc_final: 0.5938 (t80) REVERT: C 134 GLU cc_start: 0.5465 (tp30) cc_final: 0.5123 (mm-30) REVERT: C 149 ARG cc_start: 0.5839 (mtm110) cc_final: 0.4900 (mmm160) outliers start: 16 outliers final: 8 residues processed: 165 average time/residue: 1.4559 time to fit residues: 257.1178 Evaluate side-chains 156 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 146 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 155 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 4.9990 chunk 95 optimal weight: 0.0670 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 5 optimal weight: 0.0370 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN B 4 ASN B 99 ASN B 260 GLN C 116 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.170101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.137417 restraints weight = 17761.819| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.62 r_work: 0.3023 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10488 Z= 0.163 Angle : 0.525 17.060 14201 Z= 0.259 Chirality : 0.042 0.155 1601 Planarity : 0.005 0.056 1810 Dihedral : 6.284 170.146 1455 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.20 % Allowed : 16.21 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1318 helix: 1.37 (0.22), residues: 575 sheet: -0.31 (0.44), residues: 128 loop : -0.44 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 208 HIS 0.002 0.001 HIS B 555 PHE 0.011 0.001 PHE A 394 TYR 0.011 0.001 TYR A 272 ARG 0.012 0.000 ARG C 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4732.77 seconds wall clock time: 84 minutes 28.20 seconds (5068.20 seconds total)