Starting phenix.real_space_refine on Sun Mar 17 14:39:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8t_14563/03_2024/7z8t_14563.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8t_14563/03_2024/7z8t_14563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8t_14563/03_2024/7z8t_14563.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8t_14563/03_2024/7z8t_14563.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8t_14563/03_2024/7z8t_14563.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8t_14563/03_2024/7z8t_14563.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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 100 5.16 5 C 11480 2.51 5 N 3111 2.21 5 O 3383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 190": "OE1" <-> "OE2" Residue "C PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 221": "OE1" <-> "OE2" Residue "D GLU 898": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18077 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 5836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5836 Classifications: {'peptide': 720} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 707} Chain breaks: 3 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 8882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1148, 8882 Classifications: {'peptide': 1148} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 53, 'TRANS': 1094} Chain breaks: 5 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 48 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: "F" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 1708 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 243} Link IDs: {'PTRANS': 13, 'TRANS': 300} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 812 Unresolved non-hydrogen angles: 1042 Unresolved non-hydrogen dihedrals: 656 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': 12, 'GLU:plan': 14, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 418 Chain: "S" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 935 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain breaks: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 59 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 14906 SG CYS R 42 131.763 58.690 47.783 1.00 73.68 S ATOM 14925 SG CYS R 45 134.419 57.129 50.352 1.00 77.24 S ATOM 15220 SG CYS R 83 131.475 59.033 51.574 1.00 64.89 S ATOM 15149 SG CYS R 75 123.040 65.140 40.620 1.00 51.65 S ATOM 15316 SG CYS R 94 126.379 66.203 42.410 1.00 59.30 S ATOM 14992 SG CYS R 53 130.405 56.197 54.107 1.00 86.82 S ATOM 15015 SG CYS R 56 130.590 54.836 57.670 1.00 91.87 S ATOM 15099 SG CYS R 68 128.271 53.202 54.928 1.00 80.60 S Time building chain proxies: 8.67, per 1000 atoms: 0.48 Number of scatterers: 18077 At special positions: 0 Unit cell: (147.258, 154.067, 120.87, 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 100 16.00 O 3383 8.00 N 3111 7.00 C 11480 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: 6.59 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 83 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " 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 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4614 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 11 sheets defined 72.3% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'C' and resid 20 through 32 Processing helix chain 'C' and resid 38 through 55 removed outlier: 3.575A pdb=" N TYR C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS C 48 " --> pdb=" O GLU C 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASN C 51 " --> pdb=" O THR C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 105 removed outlier: 3.894A pdb=" N LYS C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 113 through 137 Processing helix chain 'C' and resid 137 through 143 removed outlier: 3.700A pdb=" N ASN C 141 " --> pdb=" O CYS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 152 Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'C' and resid 171 through 192 removed outlier: 3.592A pdb=" N LEU C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYS C 177 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLN C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 211 removed outlier: 3.671A pdb=" N GLY C 203 " --> pdb=" O ARG C 199 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 232 through 253 Processing helix chain 'C' and resid 256 through 279 removed outlier: 3.601A pdb=" N LYS C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 3.663A 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 296 Processing helix chain 'C' and resid 299 through 313 removed outlier: 3.512A pdb=" N THR C 305 " --> pdb=" O GLU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 327 Processing helix chain 'C' and resid 333 through 356 removed outlier: 3.894A pdb=" N CYS C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 4.153A 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 Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 416 through 430 removed outlier: 3.528A pdb=" N GLU C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 456 removed outlier: 3.539A pdb=" N LYS C 454 " --> pdb=" O MET C 450 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TYR C 455 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 477 removed outlier: 3.970A pdb=" N PHE C 462 " --> pdb=" O ASP C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 496 removed outlier: 3.546A pdb=" N GLU C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 526 removed outlier: 3.716A pdb=" N ARG C 506 " --> pdb=" O SER C 502 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE C 508 " --> pdb=" O LEU C 504 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C 526 " --> pdb=" O LYS C 522 " (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: 3.581A pdb=" N GLN C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 630 removed outlier: 3.935A pdb=" N ASP C 627 " --> pdb=" O GLN C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 646 Processing helix chain 'C' and resid 688 through 722 removed outlier: 4.219A pdb=" N GLN C 692 " --> pdb=" O MET C 688 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS C 693 " --> pdb=" O LYS C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 739 removed outlier: 3.779A 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 35 Processing helix chain 'D' and resid 43 through 56 removed outlier: 3.740A pdb=" N ARG D 47 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS D 51 " --> pdb=" O ARG D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'D' and resid 61 through 77 removed outlier: 3.987A pdb=" N GLY D 73 " --> pdb=" O VAL D 69 " (cutoff:3.500A) Proline residue: D 74 - end of helix removed outlier: 4.235A pdb=" N SER D 77 " --> pdb=" O GLY D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 96 removed outlier: 3.780A 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: 3.630A pdb=" N GLY D 136 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 164 removed outlier: 3.747A pdb=" N GLN D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 169 removed outlier: 3.693A pdb=" N LEU D 168 " --> pdb=" O GLN D 165 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 169 " --> pdb=" O GLY D 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 165 through 169' Processing helix chain 'D' and resid 172 through 181 Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 188 through 205 removed outlier: 3.692A pdb=" N ARG D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 224 removed outlier: 3.537A pdb=" N PHE D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 245 removed outlier: 3.730A pdb=" N THR D 231 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 251 removed outlier: 4.495A 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: 3.879A pdb=" N ASN D 265 " --> pdb=" O VAL D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 286 removed outlier: 3.627A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 3.712A 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: 3.909A pdb=" N ARG D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG D 364 " --> pdb=" O VAL D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 382 removed outlier: 4.868A 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: 3.705A 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: 4.033A pdb=" N LYS D 441 " --> pdb=" O LYS D 437 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 465 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 513 through 515 No H-bonds generated for 'chain 'D' and resid 513 through 515' Processing helix chain 'D' and resid 516 through 529 Proline residue: D 522 - end of helix Processing helix chain 'D' and resid 532 through 551 removed outlier: 3.593A pdb=" N GLN D 545 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG D 551 " --> pdb=" O VAL D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 577 removed outlier: 3.613A pdb=" N ILE D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS D 566 " --> pdb=" O THR D 562 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASP D 567 " --> pdb=" O PRO D 563 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS D 574 " --> pdb=" O THR D 570 " (cutoff:3.500A) removed outlier: 4.271A 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 619 removed outlier: 4.348A pdb=" N ASN D 610 " --> pdb=" O SER D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 637 Processing helix chain 'D' and resid 644 through 657 removed outlier: 4.951A pdb=" N GLU D 650 " --> pdb=" O PRO D 646 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL D 652 " --> pdb=" O LEU D 648 " (cutoff:3.500A) Proline residue: D 653 - end of helix removed outlier: 3.563A pdb=" N SER D 657 " --> pdb=" O PRO D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 661 removed outlier: 3.542A pdb=" N LYS D 661 " --> pdb=" O PHE D 658 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 658 through 661' Processing helix chain 'D' and resid 663 through 681 Processing helix chain 'D' and resid 682 through 685 removed outlier: 3.681A pdb=" N LEU D 685 " --> pdb=" O SER D 682 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 682 through 685' Processing helix chain 'D' and resid 686 through 695 Processing helix chain 'D' and resid 696 through 701 Proline residue: D 699 - end of helix No H-bonds generated for 'chain 'D' and resid 696 through 701' Processing helix chain 'D' and resid 706 through 723 Processing helix chain 'D' and resid 724 through 730 removed outlier: 4.294A pdb=" N SER D 728 " --> pdb=" O SER D 725 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE D 730 " --> pdb=" O LEU D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 743 removed outlier: 3.658A pdb=" N ASN D 736 " --> pdb=" O GLY D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 766 removed outlier: 3.684A pdb=" N VAL D 763 " --> pdb=" O PHE D 759 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL D 764 " --> pdb=" O GLN D 760 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR D 765 " --> pdb=" O ALA D 761 " (cutoff:3.500A) removed outlier: 3.969A 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 792 through 810 removed outlier: 4.249A pdb=" N TYR D 796 " --> pdb=" O HIS D 792 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR D 797 " --> pdb=" O LYS D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 826 Processing helix chain 'D' and resid 831 through 847 Processing helix chain 'D' and resid 856 through 866 removed outlier: 4.210A pdb=" N SER D 866 " --> pdb=" O LEU D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 887 removed outlier: 3.510A pdb=" N LYS D 873 " --> pdb=" O SER D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 902 Proline residue: D 893 - end of helix removed outlier: 3.855A pdb=" N THR D 900 " --> pdb=" O LEU D 896 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN D 902 " --> pdb=" O GLU D 898 " (cutoff:3.500A) Processing helix chain 'D' and resid 906 through 920 removed outlier: 3.603A pdb=" N HIS D 911 " --> pdb=" O TYR D 907 " (cutoff:3.500A) Processing helix chain 'D' and resid 921 through 926 removed outlier: 3.614A pdb=" N LYS D 926 " --> pdb=" O VAL D 922 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 940 Processing helix chain 'D' and resid 946 through 961 removed outlier: 3.656A pdb=" N VAL D 950 " --> pdb=" O GLY D 946 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU D 960 " --> pdb=" O GLY D 956 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE D 961 " --> pdb=" O LYS D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 973 removed outlier: 3.642A pdb=" N TYR D 973 " --> pdb=" O ARG D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 991 removed outlier: 3.700A pdb=" N ARG D 982 " --> pdb=" O SER D 978 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER D 983 " --> pdb=" O SER D 979 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS D 990 " --> pdb=" O VAL D 986 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE D 991 " --> pdb=" O THR D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1013 removed outlier: 3.701A pdb=" N ASN D1006 " --> pdb=" O PRO D1002 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLY D1009 " --> pdb=" O LYS D1005 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASP D1010 " --> pdb=" O ASN D1006 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE D1011 " --> pdb=" O CYS D1007 " (cutoff:3.500A) Processing helix chain 'D' and resid 1014 through 1016 No H-bonds generated for 'chain 'D' and resid 1014 through 1016' Processing helix chain 'D' and resid 1019 through 1037 removed outlier: 3.967A pdb=" N ARG D1023 " --> pdb=" O ASP D1019 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG D1024 " --> pdb=" O LEU D1020 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1043 removed outlier: 3.600A pdb=" N ILE D1041 " --> pdb=" O PRO D1038 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG D1042 " --> pdb=" O SER D1039 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASP D1043 " --> pdb=" O LEU D1040 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1038 through 1043' Processing helix chain 'D' and resid 1044 through 1054 Proline residue: D1050 - end of helix Processing helix chain 'D' and resid 1055 through 1057 No H-bonds generated for 'chain 'D' and resid 1055 through 1057' Processing helix chain 'D' and resid 1059 through 1061 No H-bonds generated for 'chain 'D' and resid 1059 through 1061' Processing helix chain 'D' and resid 1078 through 1093 removed outlier: 3.646A pdb=" N LEU D1093 " --> pdb=" O MET D1089 " (cutoff:3.500A) Processing helix chain 'D' and resid 1103 through 1113 Processing helix chain 'D' and resid 1116 through 1133 removed outlier: 4.042A pdb=" N THR D1132 " --> pdb=" O VAL D1128 " (cutoff:3.500A) Processing helix chain 'D' and resid 1134 through 1142 removed outlier: 4.133A pdb=" N VAL D1138 " --> pdb=" O CYS D1134 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) removed outlier: 3.518A 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: 4.141A 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 removed outlier: 3.625A pdb=" N ILE D1211 " --> pdb=" O GLU D1207 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN D1216 " --> pdb=" O PHE D1212 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 59 Processing helix chain 'R' and resid 62 through 67 removed outlier: 3.684A pdb=" N GLU R 66 " --> pdb=" O SER R 62 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 62 through 67' Processing helix chain 'R' and resid 81 through 88 Processing helix chain 'F' and resid 96 through 100 removed outlier: 3.580A pdb=" N SER F 99 " --> pdb=" O SER F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 110 Processing helix chain 'F' and resid 113 through 121 Processing helix chain 'F' and resid 124 through 131 Processing helix chain 'F' and resid 148 through 157 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: 3.542A pdb=" N LEU F 334 " --> pdb=" O GLU F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 359 Processing helix chain 'F' and resid 374 through 383 removed outlier: 3.873A pdb=" N LEU F 378 " --> pdb=" O GLY F 374 " (cutoff:3.500A) Processing helix chain 'S' and resid 18 through 22 Processing helix chain 'S' and resid 24 through 31 Processing helix chain 'S' and resid 51 through 65 Processing helix chain 'S' and resid 87 through 94 removed outlier: 4.085A pdb=" N GLU S 91 " --> pdb=" O VAL S 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 96 through 111 Processing helix chain 'S' and resid 112 through 127 Processing helix chain 'S' and resid 131 through 140 Processing helix chain 'S' and resid 146 through 157 removed outlier: 4.155A pdb=" N GLU S 150 " --> pdb=" O THR S 146 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 534 through 541 removed outlier: 6.270A pdb=" N ASP C 534 " --> pdb=" O TRP R 27 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA R 29 " --> pdb=" O ASP C 534 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER C 536 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ALA R 31 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLN C 538 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TRP R 33 " --> pdb=" O GLN C 538 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU C 540 " --> pdb=" O TRP R 33 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N TRP R 35 " --> pdb=" O LEU C 540 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 534 through 541 removed outlier: 6.270A pdb=" N ASP C 534 " --> pdb=" O TRP R 27 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA R 29 " --> pdb=" O ASP C 534 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER C 536 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ALA R 31 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLN C 538 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TRP R 33 " --> pdb=" O GLN C 538 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU C 540 " --> pdb=" O TRP R 33 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N TRP R 35 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL R 24 " --> pdb=" O VAL C 591 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL C 591 " --> pdb=" O VAL R 24 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS R 26 " --> pdb=" O GLU C 589 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 619 through 621 Processing sheet with id=AA4, first strand: chain 'C' and resid 724 through 725 Processing sheet with id=AA5, first strand: chain 'D' and resid 1063 through 1068 Processing sheet with id=AA6, first strand: chain 'R' and resid 78 through 80 removed outlier: 6.595A pdb=" N TRP R 72 " --> pdb=" O GLN R 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 139 through 141 removed outlier: 3.732A pdb=" N ARG F 164 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE F 163 " --> pdb=" O ASP F 187 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AA9, first strand: chain 'F' and resid 260 through 262 removed outlier: 3.558A pdb=" N ASN F 289 " --> pdb=" O LEU F 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 339 through 341 removed outlier: 7.343A pdb=" N LEU F 340 " --> pdb=" O GLN F 366 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 13 through 17 1113 hydrogen bonds defined for protein. 3273 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: 6.55 Time building geometry restraints manager: 7.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5098 1.33 - 1.45: 2554 1.45 - 1.57: 10561 1.57 - 1.69: 0 1.69 - 1.81: 147 Bond restraints: 18360 Sorted by residual: bond pdb=" N LEU S 105 " pdb=" CA LEU S 105 " ideal model delta sigma weight residual 1.459 1.481 -0.023 1.28e-02 6.10e+03 3.15e+00 bond pdb=" C LEU S 105 " pdb=" O LEU S 105 " ideal model delta sigma weight residual 1.236 1.216 0.020 1.26e-02 6.30e+03 2.64e+00 bond pdb=" CA LEU S 105 " pdb=" C LEU S 105 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.35e-02 5.49e+03 1.78e+00 bond pdb=" CG1 ILE S 59 " pdb=" CD1 ILE S 59 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" C ILE S 104 " pdb=" N LEU S 105 " ideal model delta sigma weight residual 1.335 1.320 0.015 1.38e-02 5.25e+03 1.13e+00 ... (remaining 18355 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.52: 411 106.52 - 113.40: 10368 113.40 - 120.29: 6481 120.29 - 127.18: 7495 127.18 - 134.07: 152 Bond angle restraints: 24907 Sorted by residual: angle pdb=" C LYS D 661 " pdb=" N ASN D 662 " pdb=" CA ASN D 662 " ideal model delta sigma weight residual 121.54 127.55 -6.01 1.91e+00 2.74e-01 9.92e+00 angle pdb=" C ILE S 104 " pdb=" N LEU S 105 " pdb=" CA LEU S 105 " ideal model delta sigma weight residual 120.31 115.62 4.69 1.52e+00 4.33e-01 9.52e+00 angle pdb=" N GLU C 705 " pdb=" CA GLU C 705 " pdb=" CB GLU C 705 " ideal model delta sigma weight residual 110.22 114.86 -4.64 1.54e+00 4.22e-01 9.08e+00 angle pdb=" C ARG C 401 " pdb=" N PHE C 402 " pdb=" CA PHE C 402 " ideal model delta sigma weight residual 122.06 116.53 5.53 1.86e+00 2.89e-01 8.85e+00 angle pdb=" N ILE C 684 " pdb=" CA ILE C 684 " pdb=" C ILE C 684 " ideal model delta sigma weight residual 112.29 109.50 2.79 9.40e-01 1.13e+00 8.81e+00 ... (remaining 24902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 10319 17.92 - 35.84: 766 35.84 - 53.76: 109 53.76 - 71.67: 25 71.67 - 89.59: 14 Dihedral angle restraints: 11233 sinusoidal: 4173 harmonic: 7060 Sorted by residual: dihedral pdb=" CA THR C 47 " pdb=" C THR C 47 " pdb=" N HIS C 48 " pdb=" CA HIS C 48 " ideal model delta harmonic sigma weight residual 180.00 158.18 21.82 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA THR S 146 " pdb=" C THR S 146 " pdb=" N GLU S 147 " pdb=" CA GLU S 147 " ideal model delta harmonic sigma weight residual -180.00 -161.68 -18.32 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA PHE C 232 " pdb=" C PHE C 232 " pdb=" N GLU C 233 " pdb=" CA GLU C 233 " ideal model delta harmonic sigma weight residual 180.00 -162.85 -17.15 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 11230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2353 0.046 - 0.092: 527 0.092 - 0.137: 99 0.137 - 0.183: 3 0.183 - 0.229: 1 Chirality restraints: 2983 Sorted by residual: chirality pdb=" CG LEU D1113 " pdb=" CB LEU D1113 " pdb=" CD1 LEU D1113 " pdb=" CD2 LEU D1113 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA GLU D 216 " pdb=" N GLU D 216 " pdb=" C GLU D 216 " pdb=" CB GLU D 216 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA ASN D 662 " pdb=" N ASN D 662 " pdb=" C ASN D 662 " pdb=" CB ASN D 662 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 2980 not shown) Planarity restraints: 3171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 814 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO D 815 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 815 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 815 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 545 " 0.025 5.00e-02 4.00e+02 3.71e-02 2.21e+00 pdb=" N PRO C 546 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 546 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 546 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 179 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO F 180 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO F 180 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 180 " 0.020 5.00e-02 4.00e+02 ... (remaining 3168 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 90 2.57 - 3.15: 14320 3.15 - 3.74: 27468 3.74 - 4.32: 35061 4.32 - 4.90: 61169 Nonbonded interactions: 138108 Sorted by model distance: nonbonded pdb=" OD2 ASP R 97 " pdb="ZN ZN R 202 " model vdw 1.988 2.230 nonbonded pdb=" O PHE S 101 " pdb=" CD1 LEU S 105 " model vdw 2.094 3.460 nonbonded pdb=" OG SER D 979 " pdb=" OD2 ASP D1019 " model vdw 2.196 2.440 nonbonded pdb=" O GLY D 819 " pdb=" NE2 GLN D 823 " model vdw 2.210 2.520 nonbonded pdb=" OD1 ASP D 582 " pdb=" N GLN D 583 " model vdw 2.251 2.520 ... (remaining 138103 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.070 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 49.790 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.090 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:11.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 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 : 0.002 0.050 18360 Z= 0.147 Angle : 0.503 9.156 24907 Z= 0.268 Chirality : 0.038 0.229 2983 Planarity : 0.004 0.043 3171 Dihedral : 13.081 89.593 6619 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.05 % Allowed : 0.21 % Favored : 99.73 % 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: 1.77 (0.18), residues: 2363 helix: 2.21 (0.14), residues: 1553 sheet: -0.84 (0.70), residues: 74 loop : -0.91 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 33 HIS 0.003 0.001 HIS D1108 PHE 0.016 0.001 PHE C 402 TYR 0.013 0.001 TYR C 377 ARG 0.006 0.000 ARG D 645 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 450 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 271 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7368 (mm-30) REVERT: C 289 ARG cc_start: 0.7026 (ttt-90) cc_final: 0.6807 (ttt-90) REVERT: C 410 LYS cc_start: 0.8022 (tttm) cc_final: 0.7734 (mtpp) REVERT: C 478 ASN cc_start: 0.8028 (p0) cc_final: 0.7659 (p0) REVERT: C 488 MET cc_start: 0.8119 (tpt) cc_final: 0.7891 (tpt) REVERT: C 565 ARG cc_start: 0.8023 (tpp80) cc_final: 0.7773 (tpp80) REVERT: D 213 ASP cc_start: 0.6820 (p0) cc_final: 0.6311 (p0) REVERT: D 216 GLU cc_start: 0.7088 (mp0) cc_final: 0.6838 (pm20) REVERT: D 362 SER cc_start: 0.8404 (p) cc_final: 0.8167 (p) REVERT: D 691 ASP cc_start: 0.6924 (m-30) cc_final: 0.6615 (m-30) REVERT: D 884 SER cc_start: 0.8208 (t) cc_final: 0.7733 (m) REVERT: D 979 SER cc_start: 0.8198 (t) cc_final: 0.7902 (t) REVERT: D 1046 ASP cc_start: 0.7409 (m-30) cc_final: 0.7169 (m-30) REVERT: D 1175 SER cc_start: 0.8070 (m) cc_final: 0.7864 (m) REVERT: R 89 LYS cc_start: 0.8655 (mtpp) cc_final: 0.8376 (tttm) outliers start: 1 outliers final: 1 residues processed: 451 average time/residue: 1.2929 time to fit residues: 650.3892 Evaluate side-chains 394 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 393 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 496 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 7.9990 chunk 179 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 95 optimal weight: 0.2980 chunk 185 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 112 optimal weight: 0.0370 chunk 138 optimal weight: 3.9990 chunk 215 optimal weight: 50.0000 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 ASN C 178 GLN C 206 GLN C 254 GLN C 638 GLN ** D 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 GLN D 431 GLN D 768 ASN D1006 ASN D1036 ASN D1140 GLN D1199 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 18360 Z= 0.181 Angle : 0.517 9.568 24907 Z= 0.264 Chirality : 0.039 0.172 2983 Planarity : 0.004 0.043 3171 Dihedral : 3.497 29.843 2541 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.46 % Allowed : 11.56 % Favored : 85.97 % 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: 1.88 (0.18), residues: 2363 helix: 2.24 (0.14), residues: 1582 sheet: -0.85 (0.68), residues: 74 loop : -0.86 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 33 HIS 0.004 0.001 HIS D1108 PHE 0.026 0.001 PHE C 402 TYR 0.016 0.001 TYR C 377 ARG 0.009 0.000 ARG D 285 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 397 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 289 ARG cc_start: 0.7038 (ttt-90) cc_final: 0.6818 (ttt-90) REVERT: C 330 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7661 (tt0) REVERT: C 451 VAL cc_start: 0.8678 (OUTLIER) cc_final: 0.8397 (p) REVERT: C 488 MET cc_start: 0.8167 (tpt) cc_final: 0.7936 (tpt) REVERT: C 565 ARG cc_start: 0.8029 (tpp80) cc_final: 0.7782 (tpp80) REVERT: D 137 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.5852 (mmm-85) REVERT: D 213 ASP cc_start: 0.6807 (p0) cc_final: 0.6117 (p0) REVERT: D 216 GLU cc_start: 0.7250 (mp0) cc_final: 0.6848 (mp0) REVERT: D 362 SER cc_start: 0.8197 (p) cc_final: 0.7942 (p) REVERT: D 696 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6999 (mt-10) REVERT: D 721 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8237 (mttt) REVERT: D 884 SER cc_start: 0.8152 (t) cc_final: 0.7714 (m) REVERT: D 953 GLU cc_start: 0.7383 (tp30) cc_final: 0.7061 (tp30) REVERT: D 1046 ASP cc_start: 0.7420 (m-30) cc_final: 0.7154 (m-30) REVERT: D 1175 SER cc_start: 0.8082 (m) cc_final: 0.7874 (m) REVERT: D 1201 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.7173 (tp40) REVERT: R 89 LYS cc_start: 0.8652 (mtpp) cc_final: 0.8386 (tttm) REVERT: S 119 THR cc_start: 0.8297 (OUTLIER) cc_final: 0.8087 (t) outliers start: 46 outliers final: 17 residues processed: 414 average time/residue: 1.3218 time to fit residues: 610.6393 Evaluate side-chains 409 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 385 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 515 LYS Chi-restraints excluded: chain C residue 548 GLN Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 760 GLU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 721 LYS Chi-restraints excluded: chain D residue 726 SER Chi-restraints excluded: chain D residue 823 GLN Chi-restraints excluded: chain D residue 931 ASN Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1201 GLN Chi-restraints excluded: chain S residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 179 optimal weight: 0.0270 chunk 146 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 215 optimal weight: 50.0000 chunk 232 optimal weight: 4.9990 chunk 192 optimal weight: 0.0070 chunk 213 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 254 GLN C 638 GLN C 685 ASN D 66 ASN D 151 GLN ** D 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 GLN D 662 ASN D 768 ASN D1140 GLN D1199 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 18360 Z= 0.174 Angle : 0.497 10.209 24907 Z= 0.253 Chirality : 0.038 0.153 2983 Planarity : 0.004 0.042 3171 Dihedral : 3.376 21.586 2539 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.84 % Allowed : 14.45 % Favored : 82.71 % 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: 1.95 (0.18), residues: 2363 helix: 2.30 (0.13), residues: 1585 sheet: -0.80 (0.67), residues: 74 loop : -0.86 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 33 HIS 0.003 0.001 HIS D1108 PHE 0.024 0.001 PHE C 402 TYR 0.021 0.001 TYR C 563 ARG 0.010 0.000 ARG D 285 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 390 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 289 ARG cc_start: 0.7052 (ttt-90) cc_final: 0.6815 (ttt-90) REVERT: C 451 VAL cc_start: 0.8715 (t) cc_final: 0.8436 (p) REVERT: C 488 MET cc_start: 0.8159 (tpt) cc_final: 0.7955 (tpt) REVERT: C 514 SER cc_start: 0.8418 (OUTLIER) cc_final: 0.8103 (p) REVERT: C 565 ARG cc_start: 0.8029 (tpp80) cc_final: 0.7685 (tpp80) REVERT: D 137 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.5887 (mmm-85) REVERT: D 213 ASP cc_start: 0.6770 (p0) cc_final: 0.6383 (p0) REVERT: D 362 SER cc_start: 0.8335 (p) cc_final: 0.8080 (p) REVERT: D 386 ARG cc_start: 0.8115 (ptt-90) cc_final: 0.7881 (ttp80) REVERT: D 627 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7875 (m) REVERT: D 696 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7012 (mt-10) REVERT: D 721 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8211 (mttt) REVERT: D 884 SER cc_start: 0.8099 (t) cc_final: 0.7639 (m) REVERT: D 953 GLU cc_start: 0.7411 (tp30) cc_final: 0.7135 (tp30) REVERT: D 971 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8289 (tttp) REVERT: D 1046 ASP cc_start: 0.7456 (m-30) cc_final: 0.7185 (m-30) REVERT: D 1201 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7107 (tp-100) REVERT: R 89 LYS cc_start: 0.8664 (mtpp) cc_final: 0.8387 (tttm) REVERT: F 129 ARG cc_start: 0.7317 (tpm-80) cc_final: 0.6980 (tpm-80) outliers start: 53 outliers final: 27 residues processed: 411 average time/residue: 1.3181 time to fit residues: 604.8983 Evaluate side-chains 417 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 383 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 548 GLN Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 683 ASP Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 721 LYS Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 726 SER Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 823 GLN Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 918 SER Chi-restraints excluded: chain D residue 931 ASN Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 971 LYS Chi-restraints excluded: chain D residue 1060 LYS Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1139 LEU Chi-restraints excluded: chain D residue 1201 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 50.0000 chunk 162 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 216 optimal weight: 20.0000 chunk 229 optimal weight: 2.9990 chunk 113 optimal weight: 0.0980 chunk 205 optimal weight: 30.0000 chunk 61 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN C 254 GLN C 361 ASN C 638 GLN C 683 ASN D 66 ASN ** D 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 GLN D 518 GLN D 662 ASN D 768 ASN D1140 GLN D1199 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18360 Z= 0.307 Angle : 0.551 10.110 24907 Z= 0.284 Chirality : 0.042 0.176 2983 Planarity : 0.004 0.045 3171 Dihedral : 3.593 19.373 2539 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.69 % Allowed : 15.36 % Favored : 80.94 % 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: 1.75 (0.18), residues: 2363 helix: 2.14 (0.13), residues: 1580 sheet: -0.78 (0.66), residues: 74 loop : -0.90 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 33 HIS 0.005 0.001 HIS D1108 PHE 0.025 0.002 PHE C 402 TYR 0.022 0.002 TYR C 377 ARG 0.007 0.000 ARG D 835 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 392 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 ASN cc_start: 0.7964 (t0) cc_final: 0.7725 (t0) REVERT: C 289 ARG cc_start: 0.7057 (ttt-90) cc_final: 0.6825 (ttt-90) REVERT: C 514 SER cc_start: 0.8409 (OUTLIER) cc_final: 0.8119 (p) REVERT: C 565 ARG cc_start: 0.8043 (tpp80) cc_final: 0.7689 (tpp80) REVERT: C 595 PHE cc_start: 0.7854 (m-80) cc_final: 0.7482 (t80) REVERT: C 641 GLN cc_start: 0.7221 (tm130) cc_final: 0.6943 (tm130) REVERT: D 67 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8067 (mt) REVERT: D 137 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.5948 (mmm-85) REVERT: D 213 ASP cc_start: 0.6822 (p0) cc_final: 0.6528 (p0) REVERT: D 362 SER cc_start: 0.8410 (p) cc_final: 0.8147 (p) REVERT: D 627 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.7999 (m) REVERT: D 696 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.7069 (mt-10) REVERT: D 721 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8307 (mttt) REVERT: D 884 SER cc_start: 0.8263 (t) cc_final: 0.7798 (m) REVERT: D 931 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7756 (m-40) REVERT: D 953 GLU cc_start: 0.7478 (tp30) cc_final: 0.7215 (tp30) REVERT: D 1046 ASP cc_start: 0.7475 (m-30) cc_final: 0.7228 (m-30) REVERT: D 1060 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7741 (tptm) REVERT: D 1201 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7076 (tp-100) REVERT: F 129 ARG cc_start: 0.7468 (tpm-80) cc_final: 0.6936 (tpm-80) outliers start: 69 outliers final: 36 residues processed: 422 average time/residue: 1.3429 time to fit residues: 634.4047 Evaluate side-chains 427 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 382 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 515 LYS Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 760 GLU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 571 CYS Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 683 ASP Chi-restraints excluded: chain D residue 684 SER Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 721 LYS Chi-restraints excluded: chain D residue 726 SER Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 823 GLN Chi-restraints excluded: chain D residue 918 SER Chi-restraints excluded: chain D residue 931 ASN Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 995 ASP Chi-restraints excluded: chain D residue 1004 LEU Chi-restraints excluded: chain D residue 1060 LYS Chi-restraints excluded: chain D residue 1074 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1139 LEU Chi-restraints excluded: chain D residue 1201 GLN Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 96 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 170 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 205 optimal weight: 30.0000 chunk 57 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN C 361 ASN C 518 ASN C 638 GLN ** D 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 662 ASN D1199 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18360 Z= 0.222 Angle : 0.521 10.203 24907 Z= 0.268 Chirality : 0.039 0.164 2983 Planarity : 0.004 0.043 3171 Dihedral : 3.540 21.063 2539 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.32 % Allowed : 16.86 % Favored : 79.82 % 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: 1.78 (0.18), residues: 2363 helix: 2.17 (0.13), residues: 1583 sheet: -0.18 (0.73), residues: 64 loop : -0.99 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 33 HIS 0.005 0.001 HIS D1051 PHE 0.022 0.001 PHE C 402 TYR 0.018 0.001 TYR D 398 ARG 0.009 0.000 ARG D 285 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 383 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 ASN cc_start: 0.7969 (t0) cc_final: 0.7733 (t0) REVERT: C 289 ARG cc_start: 0.7060 (ttt-90) cc_final: 0.6828 (ttt-90) REVERT: C 330 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: C 514 SER cc_start: 0.8404 (OUTLIER) cc_final: 0.8104 (p) REVERT: C 565 ARG cc_start: 0.8046 (tpp80) cc_final: 0.7708 (tpp80) REVERT: C 595 PHE cc_start: 0.7846 (m-80) cc_final: 0.7512 (t80) REVERT: C 641 GLN cc_start: 0.7235 (tm130) cc_final: 0.6961 (tm130) REVERT: D 67 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8075 (mt) REVERT: D 137 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.5980 (mmm-85) REVERT: D 204 MET cc_start: 0.7770 (tpp) cc_final: 0.7332 (tpp) REVERT: D 213 ASP cc_start: 0.6775 (p0) cc_final: 0.6447 (p0) REVERT: D 252 TYR cc_start: 0.8359 (m-80) cc_final: 0.8078 (m-80) REVERT: D 362 SER cc_start: 0.8356 (p) cc_final: 0.8107 (p) REVERT: D 696 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7050 (mt-10) REVERT: D 721 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8263 (mttt) REVERT: D 884 SER cc_start: 0.8217 (t) cc_final: 0.7743 (m) REVERT: D 931 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7714 (m-40) REVERT: D 953 GLU cc_start: 0.7463 (tp30) cc_final: 0.7161 (tp30) REVERT: D 1015 LEU cc_start: 0.8629 (mt) cc_final: 0.8355 (mt) REVERT: D 1046 ASP cc_start: 0.7461 (m-30) cc_final: 0.7231 (m-30) REVERT: D 1201 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.7071 (tp-100) REVERT: F 129 ARG cc_start: 0.7482 (tpm-80) cc_final: 0.6943 (tpm-80) REVERT: S 113 LYS cc_start: 0.7734 (pptt) cc_final: 0.7415 (pptt) outliers start: 62 outliers final: 41 residues processed: 411 average time/residue: 1.3160 time to fit residues: 603.1542 Evaluate side-chains 430 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 381 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 515 LYS Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 548 GLN Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 760 GLU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 345 MET Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 571 CYS Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 683 ASP Chi-restraints excluded: chain D residue 684 SER Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 721 LYS Chi-restraints excluded: chain D residue 726 SER Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 823 GLN Chi-restraints excluded: chain D residue 918 SER Chi-restraints excluded: chain D residue 931 ASN Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 995 ASP Chi-restraints excluded: chain D residue 1004 LEU Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain D residue 1201 GLN Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain S residue 96 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 0.8980 chunk 206 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 229 optimal weight: 1.9990 chunk 190 optimal weight: 0.0370 chunk 106 optimal weight: 2.9990 chunk 19 optimal weight: 0.0470 chunk 75 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 768 ASN D 998 GLN D1199 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18360 Z= 0.170 Angle : 0.501 10.796 24907 Z= 0.256 Chirality : 0.038 0.152 2983 Planarity : 0.004 0.042 3171 Dihedral : 3.441 21.424 2539 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.16 % Allowed : 17.67 % Favored : 79.18 % 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: 1.93 (0.18), residues: 2363 helix: 2.30 (0.13), residues: 1584 sheet: -0.64 (0.66), residues: 74 loop : -0.93 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 33 HIS 0.005 0.001 HIS D1051 PHE 0.019 0.001 PHE C 402 TYR 0.015 0.001 TYR C 377 ARG 0.008 0.000 ARG D 285 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 384 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 110 LEU cc_start: 0.8231 (mt) cc_final: 0.7989 (mt) REVERT: C 289 ARG cc_start: 0.7046 (ttt-90) cc_final: 0.6818 (ttt-90) REVERT: C 330 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: C 451 VAL cc_start: 0.8757 (t) cc_final: 0.8463 (p) REVERT: C 514 SER cc_start: 0.8426 (OUTLIER) cc_final: 0.8126 (p) REVERT: C 538 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7866 (mm110) REVERT: C 565 ARG cc_start: 0.8012 (tpp80) cc_final: 0.7676 (tpp80) REVERT: C 595 PHE cc_start: 0.7820 (m-80) cc_final: 0.7534 (t80) REVERT: C 641 GLN cc_start: 0.7237 (tm130) cc_final: 0.6721 (tm130) REVERT: C 762 LEU cc_start: 0.8520 (pt) cc_final: 0.8179 (pp) REVERT: C 763 GLU cc_start: 0.6704 (pp20) cc_final: 0.6472 (pp20) REVERT: D 67 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8075 (mt) REVERT: D 137 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.5973 (mmm-85) REVERT: D 204 MET cc_start: 0.7757 (tpp) cc_final: 0.7302 (tpp) REVERT: D 213 ASP cc_start: 0.6726 (p0) cc_final: 0.6483 (p0) REVERT: D 216 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: D 252 TYR cc_start: 0.8329 (m-80) cc_final: 0.8054 (m-80) REVERT: D 362 SER cc_start: 0.8295 (p) cc_final: 0.8059 (p) REVERT: D 721 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8210 (mttt) REVERT: D 884 SER cc_start: 0.8087 (t) cc_final: 0.7609 (m) REVERT: D 953 GLU cc_start: 0.7455 (tp30) cc_final: 0.7172 (tp30) REVERT: D 1015 LEU cc_start: 0.8576 (mt) cc_final: 0.8328 (mt) REVERT: D 1046 ASP cc_start: 0.7465 (m-30) cc_final: 0.7215 (m-30) REVERT: D 1201 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7043 (tp-100) REVERT: F 129 ARG cc_start: 0.7477 (tpm-80) cc_final: 0.6925 (tpm-80) REVERT: S 113 LYS cc_start: 0.7781 (pptt) cc_final: 0.7443 (pptt) outliers start: 59 outliers final: 37 residues processed: 408 average time/residue: 1.2867 time to fit residues: 587.6755 Evaluate side-chains 426 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 381 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 515 LYS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 538 GLN Chi-restraints excluded: chain C residue 548 GLN Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 760 GLU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 554 ASP Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 721 LYS Chi-restraints excluded: chain D residue 726 SER Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 823 GLN Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 918 SER Chi-restraints excluded: chain D residue 931 ASN Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 995 ASP Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1201 GLN Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain S residue 96 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 0.0370 chunk 25 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 193 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 228 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 GLN C 509 GLN C 638 GLN C 685 ASN D 217 HIS D 768 ASN D 998 GLN D1199 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18360 Z= 0.192 Angle : 0.509 11.282 24907 Z= 0.260 Chirality : 0.038 0.162 2983 Planarity : 0.004 0.043 3171 Dihedral : 3.427 21.058 2539 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.53 % Allowed : 17.34 % Favored : 79.12 % 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: 1.88 (0.18), residues: 2363 helix: 2.29 (0.13), residues: 1589 sheet: -0.63 (0.67), residues: 74 loop : -1.08 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 33 HIS 0.005 0.001 HIS D1108 PHE 0.021 0.001 PHE C 402 TYR 0.017 0.001 TYR C 377 ARG 0.007 0.000 ARG D1064 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 388 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 110 LEU cc_start: 0.8234 (mt) cc_final: 0.7985 (mt) REVERT: C 289 ARG cc_start: 0.7042 (ttt-90) cc_final: 0.6815 (ttt-90) REVERT: C 330 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: C 451 VAL cc_start: 0.8764 (t) cc_final: 0.8473 (p) REVERT: C 514 SER cc_start: 0.8425 (OUTLIER) cc_final: 0.8125 (p) REVERT: C 538 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7879 (mm110) REVERT: C 565 ARG cc_start: 0.8018 (tpp80) cc_final: 0.7688 (tpp80) REVERT: C 595 PHE cc_start: 0.7829 (m-80) cc_final: 0.7551 (t80) REVERT: C 641 GLN cc_start: 0.7246 (tm130) cc_final: 0.6969 (tm130) REVERT: C 763 GLU cc_start: 0.6657 (pp20) cc_final: 0.6417 (pp20) REVERT: D 67 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8074 (mt) REVERT: D 137 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.5992 (mmm-85) REVERT: D 252 TYR cc_start: 0.8342 (m-80) cc_final: 0.8018 (m-80) REVERT: D 362 SER cc_start: 0.8319 (p) cc_final: 0.8080 (p) REVERT: D 695 ASP cc_start: 0.7536 (m-30) cc_final: 0.7231 (m-30) REVERT: D 696 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6976 (mt-10) REVERT: D 721 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8234 (mttt) REVERT: D 863 GLU cc_start: 0.7300 (tp30) cc_final: 0.7031 (tp30) REVERT: D 884 SER cc_start: 0.8134 (t) cc_final: 0.7662 (m) REVERT: D 953 GLU cc_start: 0.7451 (tp30) cc_final: 0.7159 (tp30) REVERT: D 1015 LEU cc_start: 0.8575 (mt) cc_final: 0.8332 (mt) REVERT: D 1046 ASP cc_start: 0.7453 (m-30) cc_final: 0.7218 (m-30) REVERT: D 1201 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.7059 (tp-100) REVERT: F 129 ARG cc_start: 0.7501 (tpm-80) cc_final: 0.6960 (tpm-80) REVERT: S 113 LYS cc_start: 0.7808 (pptt) cc_final: 0.7495 (pptt) outliers start: 66 outliers final: 44 residues processed: 414 average time/residue: 1.2911 time to fit residues: 599.1088 Evaluate side-chains 437 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 385 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 515 LYS Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 538 GLN Chi-restraints excluded: chain C residue 548 GLN Chi-restraints excluded: chain C residue 597 ASN Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 554 ASP Chi-restraints excluded: chain D residue 571 CYS Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 683 ASP Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 721 LYS Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 726 SER Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 823 GLN Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 918 SER Chi-restraints excluded: chain D residue 931 ASN Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 974 LEU Chi-restraints excluded: chain D residue 995 ASP Chi-restraints excluded: chain D residue 1043 ASP Chi-restraints excluded: chain D residue 1061 GLU Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1201 GLN Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain S residue 96 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 68 optimal weight: 0.0970 chunk 44 optimal weight: 0.0170 chunk 145 optimal weight: 0.7980 chunk 155 optimal weight: 0.0070 chunk 112 optimal weight: 0.0370 chunk 21 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 207 optimal weight: 30.0000 overall best weight: 0.1512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 GLN C 206 GLN C 361 ASN C 509 GLN C 685 ASN ** D 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 431 GLN D 507 ASN D 768 ASN D1199 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18360 Z= 0.132 Angle : 0.488 10.261 24907 Z= 0.248 Chirality : 0.037 0.151 2983 Planarity : 0.004 0.042 3171 Dihedral : 3.281 22.208 2539 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.62 % Allowed : 19.38 % Favored : 78.00 % 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: 2.03 (0.18), residues: 2363 helix: 2.39 (0.13), residues: 1595 sheet: -0.52 (0.67), residues: 74 loop : -1.00 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 33 HIS 0.005 0.000 HIS D1108 PHE 0.014 0.001 PHE C 402 TYR 0.011 0.001 TYR C 278 ARG 0.010 0.000 ARG D 285 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 390 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 110 LEU cc_start: 0.8065 (mt) cc_final: 0.7805 (mt) REVERT: C 289 ARG cc_start: 0.7028 (ttt-90) cc_final: 0.6816 (ttt-90) REVERT: C 451 VAL cc_start: 0.8696 (t) cc_final: 0.8396 (t) REVERT: C 514 SER cc_start: 0.8412 (OUTLIER) cc_final: 0.8123 (p) REVERT: C 565 ARG cc_start: 0.7986 (tpp80) cc_final: 0.7631 (tpp80) REVERT: C 595 PHE cc_start: 0.7783 (m-80) cc_final: 0.7531 (t80) REVERT: C 605 THR cc_start: 0.8171 (m) cc_final: 0.7957 (t) REVERT: C 641 GLN cc_start: 0.7220 (tm130) cc_final: 0.6701 (tm130) REVERT: C 762 LEU cc_start: 0.8478 (pt) cc_final: 0.8199 (pp) REVERT: C 763 GLU cc_start: 0.6578 (pp20) cc_final: 0.6362 (pp20) REVERT: D 78 LYS cc_start: 0.7938 (mtpm) cc_final: 0.7579 (mttm) REVERT: D 204 MET cc_start: 0.7738 (tpp) cc_final: 0.7325 (tpp) REVERT: D 362 SER cc_start: 0.8162 (p) cc_final: 0.7942 (p) REVERT: D 457 MET cc_start: 0.8245 (mmm) cc_final: 0.8004 (tpp) REVERT: D 696 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7025 (mt-10) REVERT: D 953 GLU cc_start: 0.7425 (tp30) cc_final: 0.7127 (tp30) REVERT: D 1015 LEU cc_start: 0.8482 (mt) cc_final: 0.8249 (mt) REVERT: D 1046 ASP cc_start: 0.7432 (m-30) cc_final: 0.7182 (m-30) REVERT: D 1142 LEU cc_start: 0.8557 (tm) cc_final: 0.8281 (tt) REVERT: D 1201 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.7057 (tp40) REVERT: R 89 LYS cc_start: 0.8695 (mtpp) cc_final: 0.8370 (tttm) REVERT: F 129 ARG cc_start: 0.7457 (tpm-80) cc_final: 0.6862 (tpm-80) REVERT: S 113 LYS cc_start: 0.7699 (pptt) cc_final: 0.7419 (pptt) REVERT: S 126 MET cc_start: 0.6901 (mtp) cc_final: 0.6523 (mtm) outliers start: 49 outliers final: 27 residues processed: 411 average time/residue: 1.2605 time to fit residues: 579.7495 Evaluate side-chains 411 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 381 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 515 LYS Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 554 ASP Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 823 GLN Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 931 ASN Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain D residue 1175 SER Chi-restraints excluded: chain D residue 1201 GLN Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain S residue 96 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 50.0000 chunk 199 optimal weight: 0.9990 chunk 212 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 192 optimal weight: 0.8980 chunk 201 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 225 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 GLN C 254 GLN C 509 GLN C 638 GLN C 685 ASN D 66 ASN ** D 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 507 ASN D 768 ASN D1140 GLN D1199 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18360 Z= 0.270 Angle : 0.556 10.269 24907 Z= 0.284 Chirality : 0.041 0.176 2983 Planarity : 0.004 0.043 3171 Dihedral : 3.469 20.199 2539 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.46 % Allowed : 20.24 % Favored : 77.30 % 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: 1.87 (0.18), residues: 2363 helix: 2.25 (0.13), residues: 1594 sheet: -0.61 (0.67), residues: 74 loop : -1.01 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 159 HIS 0.005 0.001 HIS D1108 PHE 0.024 0.002 PHE C 402 TYR 0.020 0.002 TYR D 398 ARG 0.008 0.000 ARG D 285 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 404 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 110 LEU cc_start: 0.8265 (mt) cc_final: 0.7965 (mt) REVERT: C 289 ARG cc_start: 0.7047 (ttt-90) cc_final: 0.6829 (ttt-90) REVERT: C 514 SER cc_start: 0.8413 (OUTLIER) cc_final: 0.8114 (p) REVERT: C 538 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7940 (mm110) REVERT: C 565 ARG cc_start: 0.8009 (tpp80) cc_final: 0.7695 (tpp80) REVERT: C 595 PHE cc_start: 0.7832 (m-80) cc_final: 0.7540 (t80) REVERT: C 641 GLN cc_start: 0.7264 (tm130) cc_final: 0.6733 (tm130) REVERT: C 763 GLU cc_start: 0.6626 (pp20) cc_final: 0.6399 (pp20) REVERT: D 67 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8144 (mt) REVERT: D 78 LYS cc_start: 0.7991 (mtpm) cc_final: 0.7591 (mttm) REVERT: D 137 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.5966 (mmm-85) REVERT: D 204 MET cc_start: 0.7796 (tpp) cc_final: 0.7355 (tpp) REVERT: D 216 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: D 884 SER cc_start: 0.8149 (t) cc_final: 0.7797 (m) REVERT: D 931 ASN cc_start: 0.8052 (OUTLIER) cc_final: 0.7751 (m-40) REVERT: D 953 GLU cc_start: 0.7437 (tp30) cc_final: 0.7125 (tp30) REVERT: D 1015 LEU cc_start: 0.8560 (mt) cc_final: 0.8345 (mt) REVERT: D 1046 ASP cc_start: 0.7448 (m-30) cc_final: 0.7206 (m-30) REVERT: D 1060 LYS cc_start: 0.8104 (tptm) cc_final: 0.7415 (tptp) REVERT: D 1142 LEU cc_start: 0.8639 (tm) cc_final: 0.8366 (tt) REVERT: D 1201 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.7014 (tp-100) REVERT: F 129 ARG cc_start: 0.7528 (tpm-80) cc_final: 0.7017 (tpm-80) REVERT: S 113 LYS cc_start: 0.7795 (pptt) cc_final: 0.7483 (pptt) outliers start: 46 outliers final: 27 residues processed: 423 average time/residue: 1.3191 time to fit residues: 625.2026 Evaluate side-chains 434 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 400 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 515 LYS Chi-restraints excluded: chain C residue 538 GLN Chi-restraints excluded: chain C residue 597 ASN Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 571 CYS Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 823 GLN Chi-restraints excluded: chain D residue 918 SER Chi-restraints excluded: chain D residue 931 ASN Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1201 GLN Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain S residue 96 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 156 optimal weight: 0.6980 chunk 236 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 200 optimal weight: 10.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 GLN C 206 GLN C 509 GLN C 685 ASN ** D 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 768 ASN D1199 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18360 Z= 0.235 Angle : 0.566 12.064 24907 Z= 0.286 Chirality : 0.040 0.165 2983 Planarity : 0.004 0.046 3171 Dihedral : 3.509 20.448 2539 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.98 % Allowed : 21.63 % Favored : 76.39 % 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: 1.82 (0.18), residues: 2363 helix: 2.20 (0.13), residues: 1593 sheet: -0.09 (0.71), residues: 64 loop : -1.06 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 33 HIS 0.008 0.001 HIS D1051 PHE 0.022 0.001 PHE C 402 TYR 0.017 0.002 TYR C 278 ARG 0.012 0.000 ARG D 285 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4726 Ramachandran restraints generated. 2363 Oldfield, 0 Emsley, 2363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 395 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 110 LEU cc_start: 0.8225 (mt) cc_final: 0.7972 (mt) REVERT: C 289 ARG cc_start: 0.7063 (ttt-90) cc_final: 0.6832 (ttt-90) REVERT: C 478 ASN cc_start: 0.8044 (p0) cc_final: 0.7663 (p0) REVERT: C 514 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8119 (p) REVERT: C 565 ARG cc_start: 0.8005 (tpp80) cc_final: 0.7681 (tpp80) REVERT: C 595 PHE cc_start: 0.7823 (m-80) cc_final: 0.7576 (t80) REVERT: C 612 LEU cc_start: 0.8576 (tt) cc_final: 0.8325 (tp) REVERT: C 641 GLN cc_start: 0.7260 (tm130) cc_final: 0.6731 (tm130) REVERT: C 763 GLU cc_start: 0.6557 (pp20) cc_final: 0.6352 (pp20) REVERT: D 54 LEU cc_start: 0.8749 (mm) cc_final: 0.8545 (mp) REVERT: D 67 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8136 (mt) REVERT: D 78 LYS cc_start: 0.7987 (mtpm) cc_final: 0.7598 (mttm) REVERT: D 204 MET cc_start: 0.7779 (tpp) cc_final: 0.7356 (tpp) REVERT: D 593 MET cc_start: 0.8394 (tpp) cc_final: 0.8171 (tpt) REVERT: D 726 SER cc_start: 0.8412 (m) cc_final: 0.8159 (t) REVERT: D 729 LYS cc_start: 0.8369 (ttmm) cc_final: 0.8128 (mtmm) REVERT: D 884 SER cc_start: 0.8106 (t) cc_final: 0.7743 (m) REVERT: D 931 ASN cc_start: 0.8038 (OUTLIER) cc_final: 0.7735 (m-40) REVERT: D 953 GLU cc_start: 0.7490 (tp30) cc_final: 0.7225 (tp30) REVERT: D 1015 LEU cc_start: 0.8517 (mt) cc_final: 0.8298 (mt) REVERT: D 1046 ASP cc_start: 0.7462 (m-30) cc_final: 0.7209 (m-30) REVERT: D 1060 LYS cc_start: 0.8093 (tptm) cc_final: 0.7401 (tptp) REVERT: D 1142 LEU cc_start: 0.8629 (tm) cc_final: 0.8342 (tt) REVERT: D 1201 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.6964 (tp-100) REVERT: F 129 ARG cc_start: 0.7526 (tpm-80) cc_final: 0.6992 (tpm-80) REVERT: S 113 LYS cc_start: 0.7834 (pptt) cc_final: 0.7516 (pptt) outliers start: 37 outliers final: 29 residues processed: 408 average time/residue: 1.3327 time to fit residues: 605.1359 Evaluate side-chains 428 residues out of total 2165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 395 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 515 LYS Chi-restraints excluded: chain C residue 597 ASN Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 650 GLU Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 823 GLN Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 931 ASN Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1072 LYS Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1113 LEU Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain D residue 1201 GLN Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain S residue 96 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 193 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 GLN C 206 GLN C 509 GLN C 685 ASN ** D 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 768 ASN D1199 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.135350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.108167 restraints weight = 26164.486| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.89 r_work: 0.3229 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 18360 Z= 0.299 Angle : 0.593 12.168 24907 Z= 0.302 Chirality : 0.042 0.184 2983 Planarity : 0.004 0.051 3171 Dihedral : 3.660 21.853 2539 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.36 % Allowed : 21.36 % Favored : 76.28 % 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: 1.66 (0.18), residues: 2363 helix: 2.07 (0.13), residues: 1594 sheet: -0.12 (0.72), residues: 64 loop : -1.09 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 33 HIS 0.009 0.001 HIS D1051 PHE 0.024 0.002 PHE C 402 TYR 0.021 0.002 TYR D 398 ARG 0.012 0.000 ARG D 285 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9102.29 seconds wall clock time: 160 minutes 5.42 seconds (9605.42 seconds total)