Starting phenix.real_space_refine on Sun Mar 17 16:24:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8v_14564/03_2024/7z8v_14564.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8v_14564/03_2024/7z8v_14564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8v_14564/03_2024/7z8v_14564.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8v_14564/03_2024/7z8v_14564.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8v_14564/03_2024/7z8v_14564.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z8v_14564/03_2024/7z8v_14564.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 102 5.16 5 C 11621 2.51 5 N 3140 2.21 5 O 3447 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 706": "OD1" <-> "OD2" Residue "C ASP 754": "OD1" <-> "OD2" Residue "D ASP 147": "OD1" <-> "OD2" Residue "D ASP 160": "OD1" <-> "OD2" Residue "D ASP 267": "OD1" <-> "OD2" Residue "D ASP 486": "OD1" <-> "OD2" Residue "D ASP 554": "OD1" <-> "OD2" Residue "D ASP 683": "OD1" <-> "OD2" Residue "D ASP 1019": "OD1" <-> "OD2" Residue "D ASP 1170": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18313 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 5893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5893 Classifications: {'peptide': 726} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 713} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 8982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1158, 8982 Classifications: {'peptide': 1158} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 55, 'TRANS': 1102} Chain breaks: 3 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 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: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 1728 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 237} Link IDs: {'PTRANS': 13, 'TRANS': 300} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 791 Unresolved non-hydrogen angles: 1017 Unresolved non-hydrogen dihedrals: 637 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 13, 'TYR:plan': 3, 'ASN:plan1': 14, 'TRP:plan': 2, 'HIS:plan': 10, 'PHE:plan': 11, 'GLU:plan': 12, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 404 Chain: "S" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 994 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain breaks: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 45 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 15063 SG CYS R 42 136.885 54.531 49.334 1.00 72.48 S ATOM 15082 SG CYS R 45 139.140 52.701 52.097 1.00 76.62 S ATOM 15377 SG CYS R 83 136.157 54.683 53.076 1.00 64.65 S ATOM 15306 SG CYS R 75 129.834 62.575 41.901 1.00 49.02 S ATOM 15473 SG CYS R 94 132.944 63.086 44.257 1.00 56.21 S ATOM 15149 SG CYS R 53 134.471 51.590 55.315 1.00 83.93 S ATOM 15172 SG CYS R 56 133.871 49.886 58.679 1.00 86.67 S ATOM 15256 SG CYS R 68 131.941 48.803 55.413 1.00 80.23 S Time building chain proxies: 10.28, per 1000 atoms: 0.56 Number of scatterers: 18313 At special positions: 0 Unit cell: (151.514, 154.918, 118.317, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 102 16.00 O 3447 8.00 N 3140 7.00 C 11621 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: 6.73 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " 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 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4652 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 10 sheets defined 71.2% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'C' and resid 20 through 32 Processing helix chain 'C' and resid 38 through 54 Processing helix chain 'C' and resid 87 through 105 removed outlier: 3.883A pdb=" N LYS C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 137 removed outlier: 3.578A pdb=" N ASP C 125 " --> pdb=" O GLN C 121 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE C 128 " --> pdb=" O GLU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 152 removed outlier: 4.559A pdb=" N VAL C 145 " --> pdb=" O ASN C 141 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ARG C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'C' and resid 175 through 192 Processing helix chain 'C' and resid 198 through 211 removed outlier: 3.802A pdb=" N GLY C 203 " --> pdb=" O ARG C 199 " (cutoff:3.500A) removed outlier: 4.426A 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 255 Processing helix chain 'C' and resid 256 through 279 removed outlier: 3.662A pdb=" N LYS C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 283 through 297 Processing helix chain 'C' and resid 299 through 313 removed outlier: 3.529A 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 354 Processing helix chain 'C' and resid 355 through 361 removed outlier: 3.911A pdb=" N ALA C 358 " --> pdb=" O CYS C 355 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C 359 " --> pdb=" O GLY C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 385 Processing helix chain 'C' and resid 388 through 405 removed outlier: 3.779A pdb=" N ASN C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 416 through 431 removed outlier: 3.638A pdb=" N GLU C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 454 removed outlier: 3.617A pdb=" N LYS C 454 " --> pdb=" O MET C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 477 removed outlier: 3.937A pdb=" N PHE C 462 " --> pdb=" O ASP C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 496 removed outlier: 3.652A pdb=" N GLU C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 527 removed outlier: 3.749A pdb=" N MET C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY C 512 " --> pdb=" O PHE C 508 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR C 526 " --> pdb=" O LYS C 522 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASN C 527 " --> pdb=" O LYS C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 574 Processing helix chain 'C' and resid 605 through 613 Processing helix chain 'C' and resid 622 through 630 Processing helix chain 'C' and resid 632 through 646 Processing helix chain 'C' and resid 688 through 722 removed outlier: 4.258A pdb=" N GLN C 692 " --> pdb=" O MET C 688 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS C 693 " --> pdb=" O LYS C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 739 Processing helix chain 'C' and resid 745 through 759 Processing helix chain 'D' and resid 6 through 15 Processing helix chain 'D' and resid 19 through 36 Processing helix chain 'D' and resid 42 through 57 removed outlier: 3.831A pdb=" N GLU D 46 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG D 47 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 78 removed outlier: 4.108A pdb=" N GLY D 73 " --> pdb=" O VAL D 69 " (cutoff:3.500A) Proline residue: D 74 - end of helix removed outlier: 4.209A pdb=" N SER D 77 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS D 78 " --> pdb=" O PRO D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 96 removed outlier: 3.733A pdb=" N VAL D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR D 86 " --> pdb=" O TYR D 82 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU D 96 " --> pdb=" O CYS D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 117 removed outlier: 3.531A pdb=" N LEU D 117 " --> pdb=" O VAL D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 144 removed outlier: 3.737A pdb=" N SER D 140 " --> pdb=" O GLY D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 164 removed outlier: 3.676A pdb=" N ARG D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 172 through 181 Processing helix chain 'D' and resid 182 through 186 removed outlier: 3.540A pdb=" N THR D 185 " --> pdb=" O PRO D 182 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER D 186 " --> pdb=" O GLN D 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 182 through 186' Processing helix chain 'D' and resid 188 through 205 removed outlier: 3.590A pdb=" N ARG D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 224 removed outlier: 3.548A pdb=" N LYS D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 245 removed outlier: 3.539A pdb=" N THR D 231 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 251 removed outlier: 4.427A 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: 3.865A pdb=" N ASN D 265 " --> pdb=" O VAL D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 286 Processing helix chain 'D' and resid 287 through 292 removed outlier: 3.682A pdb=" N VAL D 290 " --> pdb=" O PRO D 287 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR D 291 " --> pdb=" O LYS D 288 " (cutoff:3.500A) Proline residue: D 292 - end of helix No H-bonds generated for 'chain 'D' and resid 287 through 292' Processing helix chain 'D' and resid 293 through 306 removed outlier: 4.332A pdb=" N THR D 306 " --> pdb=" O LEU D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 364 removed outlier: 3.872A pdb=" N ARG D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 382 removed outlier: 4.932A 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: 3.883A pdb=" N ARG D 406 " --> pdb=" O LEU D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 443 Proline residue: D 433 - end of helix removed outlier: 3.973A pdb=" N LYS D 441 " --> pdb=" O LYS D 437 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 465 removed outlier: 3.569A pdb=" N ARG D 451 " --> pdb=" O SER D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 Proline residue: D 478 - end of helix Processing helix chain 'D' and resid 490 through 507 Processing helix chain 'D' and resid 508 through 515 removed outlier: 6.112A pdb=" N GLN D 511 " --> pdb=" O HIS D 508 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL D 512 " --> pdb=" O SER D 509 " (cutoff:3.500A) Proline residue: D 515 - end of helix Processing helix chain 'D' and resid 516 through 529 Proline residue: D 522 - end of helix removed outlier: 3.607A pdb=" N GLY D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 551 removed outlier: 3.531A pdb=" N GLU D 538 " --> pdb=" O LYS D 534 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN D 545 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG D 551 " --> pdb=" O VAL D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 563 No H-bonds generated for 'chain 'D' and resid 561 through 563' Processing helix chain 'D' and resid 564 through 577 removed outlier: 3.579A pdb=" N LEU D 568 " --> pdb=" O TYR D 564 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS D 574 " --> pdb=" O THR D 570 " (cutoff:3.500A) removed outlier: 4.131A 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: 4.525A 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 658 removed outlier: 3.585A pdb=" N LEU D 648 " --> pdb=" O LEU D 644 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY D 649 " --> pdb=" O ARG D 645 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLU D 650 " --> pdb=" O PRO D 646 " (cutoff:3.500A) Proline residue: D 653 - end of helix removed outlier: 3.508A pdb=" N PHE D 658 " --> pdb=" O ILE D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 681 Processing helix chain 'D' and resid 682 through 685 Processing helix chain 'D' and resid 686 through 695 removed outlier: 4.472A pdb=" N ALA D 692 " --> pdb=" O ALA D 688 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL D 693 " --> pdb=" O MET D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 701 Processing helix chain 'D' and resid 705 through 723 removed outlier: 3.693A pdb=" N SER D 709 " --> pdb=" O ASP D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 731 removed outlier: 4.299A pdb=" N SER D 728 " --> pdb=" O SER D 725 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS D 729 " --> pdb=" O SER D 726 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 730 " --> pdb=" O LEU D 727 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER D 731 " --> pdb=" O SER D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 743 removed outlier: 3.573A pdb=" N ASN D 736 " --> pdb=" O GLY D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 766 removed outlier: 3.828A pdb=" N VAL D 764 " --> pdb=" O GLN D 760 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR D 765 " --> pdb=" O ALA D 761 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 786 Proline residue: D 782 - end of helix Processing helix chain 'D' and resid 793 through 810 removed outlier: 3.688A pdb=" N TYR D 797 " --> pdb=" O LYS D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 826 removed outlier: 3.694A pdb=" N VAL D 817 " --> pdb=" O GLU D 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 849 removed outlier: 4.386A pdb=" N HIS D 848 " --> pdb=" O GLU D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 864 removed outlier: 3.631A pdb=" N ALA D 864 " --> pdb=" O VAL D 860 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 887 removed outlier: 3.539A pdb=" N SER D 884 " --> pdb=" O LEU D 880 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL D 885 " --> pdb=" O GLY D 881 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY D 886 " --> pdb=" O SER D 882 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN D 887 " --> pdb=" O ILE D 883 " (cutoff:3.500A) Processing helix chain 'D' and resid 891 through 902 removed outlier: 3.914A pdb=" N THR D 900 " --> pdb=" O LEU D 896 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN D 902 " --> pdb=" O GLU D 898 " (cutoff:3.500A) Processing helix chain 'D' and resid 908 through 919 Processing helix chain 'D' and resid 921 through 926 Processing helix chain 'D' and resid 928 through 940 removed outlier: 3.559A pdb=" N LYS D 938 " --> pdb=" O ALA D 934 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS D 939 " --> pdb=" O LEU D 935 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 961 removed outlier: 3.598A pdb=" N VAL D 950 " --> pdb=" O GLY D 946 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 960 " --> pdb=" O GLY D 956 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE D 961 " --> pdb=" O LYS D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 972 Processing helix chain 'D' and resid 978 through 991 removed outlier: 3.516A pdb=" N ARG D 982 " --> pdb=" O SER D 978 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 983 " --> pdb=" O SER D 979 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS D 990 " --> pdb=" O VAL D 986 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE D 991 " --> pdb=" O THR D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1013 removed outlier: 3.864A pdb=" N ASN D1006 " --> pdb=" O PRO D1002 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS D1007 " --> pdb=" O LEU D1003 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N GLY D1009 " --> pdb=" O LYS D1005 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ASP D1010 " --> pdb=" O ASN D1006 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE D1011 " --> pdb=" O CYS D1007 " (cutoff:3.500A) Processing helix chain 'D' and resid 1014 through 1017 Processing helix chain 'D' and resid 1019 through 1037 removed outlier: 3.847A pdb=" N ARG D1023 " --> pdb=" O ASP D1019 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG D1024 " --> pdb=" O LEU D1020 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1043 removed outlier: 4.461A 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) Processing helix chain 'D' and resid 1044 through 1055 Proline residue: D1050 - end of helix 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 1095 removed outlier: 3.735A pdb=" N LEU D1093 " --> pdb=" O MET D1089 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP D1094 " --> pdb=" O TYR D1090 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER D1095 " --> pdb=" O THR D1091 " (cutoff:3.500A) Processing helix chain 'D' and resid 1101 through 1113 removed outlier: 3.812A pdb=" N PHE D1105 " --> pdb=" O ASP D1101 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1133 removed outlier: 3.519A pdb=" N LEU D1122 " --> pdb=" O ASP D1118 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU D1125 " --> pdb=" O MET D1121 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR D1132 " --> pdb=" O VAL D1128 " (cutoff:3.500A) Processing helix chain 'D' and resid 1134 through 1141 removed outlier: 4.015A pdb=" N VAL D1138 " --> pdb=" O CYS D1134 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG D1141 " --> pdb=" O ALA D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1155 Proline residue: D1148 - end of helix Processing helix chain 'D' and resid 1162 through 1185 removed outlier: 3.625A pdb=" N PHE D1166 " --> pdb=" O VAL D1162 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR D1185 " --> pdb=" O ALA D1181 " (cutoff:3.500A) Processing helix chain 'D' and resid 1192 through 1205 removed outlier: 3.732A pdb=" N GLU D1197 " --> pdb=" O PRO D1193 " (cutoff:3.500A) Processing helix chain 'D' and resid 1205 through 1215 removed outlier: 3.506A pdb=" N ILE D1211 " --> pdb=" O GLU D1207 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D1215 " --> pdb=" O ILE D1211 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 59 Processing helix chain 'R' and resid 62 through 67 removed outlier: 3.593A pdb=" N GLU R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 88 Processing helix chain '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 158 Processing helix chain 'F' and resid 194 through 203 Processing helix chain 'F' and resid 219 through 227 Processing helix chain 'F' and resid 244 through 255 Processing helix chain 'F' and resid 270 through 280 Processing helix chain 'F' and resid 298 through 309 Processing helix chain 'F' and resid 324 through 334 removed outlier: 3.527A 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: 3.910A 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 29 Processing helix chain 'S' and resid 51 through 65 Processing helix chain 'S' and resid 87 through 94 Processing helix chain 'S' and resid 96 through 111 Processing helix chain 'S' and resid 112 through 127 Processing helix chain 'S' and resid 131 through 140 Processing helix chain 'S' and resid 146 through 157 Processing sheet with id=AA1, first strand: chain 'C' and resid 534 through 541 removed outlier: 6.192A pdb=" N ASP C 534 " --> pdb=" O TRP R 27 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ALA R 29 " --> pdb=" O ASP C 534 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER C 536 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ALA R 31 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N GLN C 538 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N TRP R 33 " --> pdb=" O GLN C 538 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU C 540 " --> pdb=" O TRP R 33 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N TRP R 35 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N PHE R 22 " --> pdb=" O LEU C 590 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LEU C 590 " --> pdb=" O PHE R 22 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N VAL R 24 " --> pdb=" O GLY C 588 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N GLY C 588 " --> pdb=" O VAL R 24 " (cutoff:3.500A) removed outlier: 11.498A pdb=" N LYS R 26 " --> pdb=" O SER C 586 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N SER C 586 " --> pdb=" O LYS R 26 " (cutoff:3.500A) removed outlier: 11.156A pdb=" N ASN R 28 " --> pdb=" O GLN C 584 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N GLN C 584 " --> pdb=" O ASN R 28 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL R 30 " --> pdb=" O LEU C 582 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR C 599 " --> pdb=" O THR C 592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 619 through 621 Processing sheet with id=AA3, first strand: chain 'C' and resid 724 through 726 Processing sheet with id=AA4, first strand: chain 'D' and resid 1063 through 1068 Processing sheet with id=AA5, first strand: chain 'R' and resid 78 through 80 removed outlier: 6.643A pdb=" N TRP R 72 " --> pdb=" O GLN R 104 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 139 through 141 removed outlier: 3.521A pdb=" N ARG F 164 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET F 186 " --> pdb=" O ASN F 210 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER F 212 " --> pdb=" O MET F 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AA8, first strand: chain 'F' and resid 260 through 262 Processing sheet with id=AA9, first strand: chain 'F' and resid 339 through 341 removed outlier: 7.353A pdb=" N LEU F 340 " --> pdb=" O GLN F 366 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 13 through 17 1118 hydrogen bonds defined for protein. 3288 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: 5.94 Time building geometry restraints manager: 7.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6054 1.34 - 1.46: 2797 1.46 - 1.58: 9603 1.58 - 1.69: 0 1.69 - 1.81: 149 Bond restraints: 18603 Sorted by residual: bond pdb=" CA ASN C 478 " pdb=" CB ASN C 478 " ideal model delta sigma weight residual 1.527 1.555 -0.028 2.48e-02 1.63e+03 1.25e+00 bond pdb=" CB PRO C 556 " pdb=" CG PRO C 556 " ideal model delta sigma weight residual 1.492 1.548 -0.056 5.00e-02 4.00e+02 1.25e+00 bond pdb=" C SER F 179 " pdb=" N PRO F 180 " ideal model delta sigma weight residual 1.331 1.345 -0.014 1.27e-02 6.20e+03 1.16e+00 bond pdb=" CB ASN C 683 " pdb=" CG ASN C 683 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.05e-01 bond pdb=" CG LEU C 116 " pdb=" CD1 LEU C 116 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.11e-01 ... (remaining 18598 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.43: 417 106.43 - 113.33: 10426 113.33 - 120.23: 6556 120.23 - 127.13: 7680 127.13 - 134.03: 155 Bond angle restraints: 25234 Sorted by residual: angle pdb=" N GLU D1171 " pdb=" CA GLU D1171 " pdb=" CB GLU D1171 " ideal model delta sigma weight residual 110.28 115.46 -5.18 1.55e+00 4.16e-01 1.11e+01 angle pdb=" CA LEU D1184 " pdb=" CB LEU D1184 " pdb=" CG LEU D1184 " ideal model delta sigma weight residual 116.30 127.10 -10.80 3.50e+00 8.16e-02 9.52e+00 angle pdb=" C LYS D 661 " pdb=" N ASN D 662 " pdb=" CA ASN D 662 " ideal model delta sigma weight residual 121.54 127.28 -5.74 1.91e+00 2.74e-01 9.03e+00 angle pdb=" C GLY C 85 " pdb=" N LEU C 86 " pdb=" CA LEU C 86 " ideal model delta sigma weight residual 121.54 127.27 -5.73 1.91e+00 2.74e-01 8.99e+00 angle pdb=" C VAL R 39 " pdb=" N ASP R 40 " pdb=" CA ASP R 40 " ideal model delta sigma weight residual 121.54 126.86 -5.32 1.91e+00 2.74e-01 7.74e+00 ... (remaining 25229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10311 17.95 - 35.90: 894 35.90 - 53.85: 139 53.85 - 71.80: 34 71.80 - 89.75: 14 Dihedral angle restraints: 11392 sinusoidal: 4268 harmonic: 7124 Sorted by residual: dihedral pdb=" CA MET C 111 " pdb=" C MET C 111 " pdb=" N ASP C 112 " pdb=" CA ASP C 112 " ideal model delta harmonic sigma weight residual -180.00 -160.59 -19.41 0 5.00e+00 4.00e-02 1.51e+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 -162.54 -17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CB GLU D 270 " pdb=" CG GLU D 270 " pdb=" CD GLU D 270 " pdb=" OE1 GLU D 270 " ideal model delta sinusoidal sigma weight residual 0.00 -88.96 88.96 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 11389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1962 0.032 - 0.064: 746 0.064 - 0.096: 216 0.096 - 0.129: 80 0.129 - 0.161: 5 Chirality restraints: 3009 Sorted by residual: chirality pdb=" CA GLU S 102 " pdb=" N GLU S 102 " pdb=" C GLU S 102 " pdb=" CB GLU S 102 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA TYR C 377 " pdb=" N TYR C 377 " pdb=" C TYR C 377 " pdb=" CB TYR C 377 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.54e-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 5.20e-01 ... (remaining 3006 not shown) Planarity restraints: 3221 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 555 " -0.068 5.00e-02 4.00e+02 1.03e-01 1.68e+01 pdb=" N PRO C 556 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO C 556 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 556 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 173 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO D 174 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 174 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 174 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 545 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO C 546 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 546 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 546 " 0.027 5.00e-02 4.00e+02 ... (remaining 3218 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 73 2.57 - 3.15: 14436 3.15 - 3.74: 27764 3.74 - 4.32: 35852 4.32 - 4.90: 62212 Nonbonded interactions: 140337 Sorted by model distance: nonbonded pdb=" OD2 ASP R 97 " pdb="ZN ZN R 202 " model vdw 1.989 2.230 nonbonded pdb=" OG SER S 8 " pdb=" OD1 ASP S 10 " model vdw 2.276 2.440 nonbonded pdb=" NH1 ARG C 127 " pdb=" OE1 GLU C 210 " model vdw 2.310 2.520 nonbonded pdb=" OH TYR D 372 " pdb=" OG1 THR D 405 " model vdw 2.318 2.440 nonbonded pdb=" OE1 GLU C 190 " pdb=" OH TYR C 278 " model vdw 2.331 2.440 ... (remaining 140332 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.370 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 50.070 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18603 Z= 0.174 Angle : 0.507 10.798 25234 Z= 0.270 Chirality : 0.039 0.161 3009 Planarity : 0.004 0.103 3221 Dihedral : 13.968 89.753 6740 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 1.51 (0.18), residues: 2391 helix: 2.05 (0.14), residues: 1543 sheet: -1.33 (0.64), residues: 78 loop : -0.93 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 88 HIS 0.004 0.001 HIS D1108 PHE 0.019 0.001 PHE C 402 TYR 0.018 0.001 TYR C 377 ARG 0.006 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 437 time to evaluate : 2.087 Fit side-chains REVERT: C 331 ASP cc_start: 0.7154 (t0) cc_final: 0.6848 (t0) REVERT: C 763 GLU cc_start: 0.6859 (pp20) cc_final: 0.6107 (pp20) REVERT: D 429 GLN cc_start: 0.7920 (tp-100) cc_final: 0.7650 (mm-40) REVERT: D 593 MET cc_start: 0.8362 (tpp) cc_final: 0.8124 (tpp) REVERT: D 1171 GLU cc_start: 0.7115 (mp0) cc_final: 0.6529 (mp0) REVERT: S 88 TRP cc_start: 0.5836 (t60) cc_final: 0.4493 (t60) outliers start: 0 outliers final: 1 residues processed: 437 average time/residue: 1.2755 time to fit residues: 622.9035 Evaluate side-chains 389 residues out of total 2183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 388 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 850 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 201 optimal weight: 9.9990 chunk 181 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 122 optimal weight: 0.0570 chunk 96 optimal weight: 0.0270 chunk 187 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 217 optimal weight: 50.0000 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN C 206 GLN C 448 GLN C 505 GLN C 520 GLN C 615 ASN C 641 GLN D 66 ASN D 83 GLN D 599 ASN D 663 GLN D 823 GLN D 931 ASN D1199 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18603 Z= 0.196 Angle : 0.503 7.805 25234 Z= 0.266 Chirality : 0.039 0.166 3009 Planarity : 0.004 0.068 3221 Dihedral : 3.633 42.011 2568 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.78 % Allowed : 10.44 % Favored : 87.78 % 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: 1.70 (0.18), residues: 2391 helix: 2.16 (0.14), residues: 1572 sheet: -0.95 (0.66), residues: 80 loop : -0.93 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 88 HIS 0.004 0.001 HIS D1108 PHE 0.022 0.001 PHE D 894 TYR 0.020 0.001 TYR C 377 ARG 0.004 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 406 time to evaluate : 2.198 Fit side-chains revert: symmetry clash REVERT: C 331 ASP cc_start: 0.7168 (t0) cc_final: 0.6863 (t0) REVERT: C 478 ASN cc_start: 0.8060 (p0) cc_final: 0.7769 (p0) REVERT: D 34 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7755 (mp) REVERT: D 48 LYS cc_start: 0.7631 (mtmp) cc_final: 0.7378 (mtmp) REVERT: D 429 GLN cc_start: 0.7889 (tp-100) cc_final: 0.7619 (mm-40) REVERT: D 593 MET cc_start: 0.8483 (tpp) cc_final: 0.8262 (tpp) REVERT: D 748 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7746 (pt0) REVERT: D 890 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6964 (tm-30) REVERT: D 1081 ILE cc_start: 0.8150 (mt) cc_final: 0.7869 (mm) REVERT: D 1171 GLU cc_start: 0.7139 (mp0) cc_final: 0.6541 (mp0) REVERT: F 127 TRP cc_start: 0.7656 (m-10) cc_final: 0.7422 (m-10) outliers start: 34 outliers final: 12 residues processed: 414 average time/residue: 1.2490 time to fit residues: 579.2405 Evaluate side-chains 407 residues out of total 2183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 392 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 748 GLN Chi-restraints excluded: chain D residue 890 GLU Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 965 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain F residue 117 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 120 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 217 optimal weight: 40.0000 chunk 234 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN C 206 GLN C 448 GLN C 520 GLN D 66 ASN D 83 GLN D 931 ASN D1199 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18603 Z= 0.215 Angle : 0.493 7.996 25234 Z= 0.260 Chirality : 0.040 0.166 3009 Planarity : 0.004 0.056 3221 Dihedral : 3.548 17.793 2566 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.15 % Allowed : 12.53 % Favored : 85.32 % 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: 2391 helix: 2.19 (0.13), residues: 1574 sheet: -0.92 (0.65), residues: 78 loop : -0.89 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 33 HIS 0.005 0.001 HIS D1108 PHE 0.020 0.002 PHE C 402 TYR 0.020 0.001 TYR C 377 ARG 0.003 0.000 ARG D 743 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 412 time to evaluate : 2.189 Fit side-chains revert: symmetry clash REVERT: C 175 LEU cc_start: 0.7796 (mt) cc_final: 0.7543 (mt) REVERT: C 331 ASP cc_start: 0.7166 (t0) cc_final: 0.6888 (t0) REVERT: C 478 ASN cc_start: 0.8025 (p0) cc_final: 0.7717 (p0) REVERT: D 429 GLN cc_start: 0.7913 (tp-100) cc_final: 0.7637 (mm-40) REVERT: D 593 MET cc_start: 0.8479 (tpp) cc_final: 0.8272 (tpp) REVERT: D 748 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7744 (pt0) REVERT: D 890 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.7008 (tm-30) REVERT: D 1081 ILE cc_start: 0.8166 (mt) cc_final: 0.7927 (mm) REVERT: F 127 TRP cc_start: 0.7744 (m-10) cc_final: 0.7503 (m-10) outliers start: 41 outliers final: 17 residues processed: 426 average time/residue: 1.2557 time to fit residues: 599.0993 Evaluate side-chains 417 residues out of total 2183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 398 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 748 GLN Chi-restraints excluded: chain D residue 890 GLU Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 965 THR Chi-restraints excluded: chain D residue 1074 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 134 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 214 optimal weight: 50.0000 chunk 163 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 218 optimal weight: 10.0000 chunk 231 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 206 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 48 HIS C 98 ASN C 206 GLN C 368 GLN C 448 GLN C 641 GLN D 66 ASN D 83 GLN D 823 GLN D 931 ASN R 48 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18603 Z= 0.312 Angle : 0.542 9.468 25234 Z= 0.283 Chirality : 0.042 0.179 3009 Planarity : 0.004 0.050 3221 Dihedral : 3.696 19.031 2566 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.36 % Allowed : 14.58 % Favored : 83.06 % 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: 1.62 (0.18), residues: 2391 helix: 2.07 (0.13), residues: 1572 sheet: -0.98 (0.64), residues: 80 loop : -0.89 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 33 HIS 0.006 0.001 HIS D1116 PHE 0.021 0.002 PHE C 402 TYR 0.024 0.002 TYR C 377 ARG 0.004 0.000 ARG C 424 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 415 time to evaluate : 2.171 Fit side-chains REVERT: C 259 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7194 (mm-30) REVERT: C 331 ASP cc_start: 0.7172 (t0) cc_final: 0.6915 (t0) REVERT: C 478 ASN cc_start: 0.8021 (p0) cc_final: 0.7724 (p0) REVERT: D 351 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7321 (ttm-80) REVERT: D 429 GLN cc_start: 0.8018 (tp-100) cc_final: 0.7723 (mm-40) REVERT: D 748 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7718 (pt0) REVERT: D 890 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6924 (tm-30) REVERT: D 1025 VAL cc_start: 0.8208 (t) cc_final: 0.7989 (m) REVERT: D 1081 ILE cc_start: 0.8215 (mt) cc_final: 0.8015 (mm) REVERT: D 1171 GLU cc_start: 0.7029 (mp0) cc_final: 0.6742 (mp0) REVERT: F 127 TRP cc_start: 0.7805 (m-10) cc_final: 0.7564 (m-10) REVERT: S 88 TRP cc_start: 0.5884 (t60) cc_final: 0.4436 (t60) outliers start: 45 outliers final: 23 residues processed: 426 average time/residue: 1.2617 time to fit residues: 600.4152 Evaluate side-chains 426 residues out of total 2183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 400 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 597 ASN Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 351 ARG Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 748 GLN Chi-restraints excluded: chain D residue 890 GLU Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 965 THR Chi-restraints excluded: chain D residue 1074 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 134 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 192 optimal weight: 2.9990 chunk 131 optimal weight: 0.0570 chunk 3 optimal weight: 0.0040 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 197 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 overall best weight: 0.7712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN C 448 GLN C 520 GLN C 641 GLN D 83 GLN D 244 GLN D 823 GLN D 931 ASN R 28 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18603 Z= 0.204 Angle : 0.498 8.485 25234 Z= 0.261 Chirality : 0.039 0.211 3009 Planarity : 0.004 0.046 3221 Dihedral : 3.618 20.695 2566 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.78 % Allowed : 15.21 % Favored : 82.01 % 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: 1.74 (0.18), residues: 2391 helix: 2.17 (0.13), residues: 1574 sheet: -0.96 (0.64), residues: 80 loop : -0.86 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 33 HIS 0.005 0.001 HIS D1108 PHE 0.018 0.001 PHE C 569 TYR 0.021 0.001 TYR C 377 ARG 0.004 0.000 ARG D 743 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 411 time to evaluate : 2.073 Fit side-chains REVERT: C 331 ASP cc_start: 0.7163 (t0) cc_final: 0.6904 (t0) REVERT: C 478 ASN cc_start: 0.7933 (p0) cc_final: 0.7675 (p0) REVERT: C 750 LYS cc_start: 0.7654 (mttp) cc_final: 0.7424 (mttp) REVERT: D 429 GLN cc_start: 0.7990 (tp-100) cc_final: 0.7703 (mm-40) REVERT: D 695 ASP cc_start: 0.7304 (m-30) cc_final: 0.7092 (m-30) REVERT: D 748 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7718 (pt0) REVERT: D 890 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6896 (tm-30) REVERT: F 127 TRP cc_start: 0.7809 (m-10) cc_final: 0.7537 (m100) REVERT: S 88 TRP cc_start: 0.5829 (t60) cc_final: 0.4343 (t60) outliers start: 53 outliers final: 30 residues processed: 430 average time/residue: 1.2294 time to fit residues: 593.9602 Evaluate side-chains 434 residues out of total 2183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 402 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 522 LYS Chi-restraints excluded: chain C residue 597 ASN Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 621 ASN Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 725 SER Chi-restraints excluded: chain D residue 748 GLN Chi-restraints excluded: chain D residue 890 GLU Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 944 GLU Chi-restraints excluded: chain D residue 965 THR Chi-restraints excluded: chain D residue 1074 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain D residue 1204 SER Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 179 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 77 optimal weight: 0.0040 chunk 208 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 520 GLN D 66 ASN D 83 GLN D 823 GLN D 931 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18603 Z= 0.219 Angle : 0.501 8.455 25234 Z= 0.262 Chirality : 0.040 0.205 3009 Planarity : 0.004 0.045 3221 Dihedral : 3.576 18.013 2566 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.73 % Allowed : 16.15 % Favored : 81.12 % 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: 1.78 (0.18), residues: 2391 helix: 2.19 (0.13), residues: 1574 sheet: -1.01 (0.63), residues: 81 loop : -0.82 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 33 HIS 0.005 0.001 HIS D1108 PHE 0.019 0.002 PHE C 569 TYR 0.021 0.002 TYR S 109 ARG 0.004 0.000 ARG D 743 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 404 time to evaluate : 2.081 Fit side-chains REVERT: C 331 ASP cc_start: 0.7158 (t0) cc_final: 0.6904 (t0) REVERT: C 478 ASN cc_start: 0.7927 (p0) cc_final: 0.7646 (p0) REVERT: C 750 LYS cc_start: 0.7654 (mttp) cc_final: 0.7441 (mttp) REVERT: D 351 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7369 (ttm-80) REVERT: D 406 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6729 (tpt90) REVERT: D 429 GLN cc_start: 0.8014 (tp-100) cc_final: 0.7714 (mm-40) REVERT: D 748 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7737 (pt0) REVERT: D 890 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: D 1072 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7935 (tptp) REVERT: F 127 TRP cc_start: 0.7825 (m-10) cc_final: 0.7565 (m100) REVERT: S 88 TRP cc_start: 0.5841 (t60) cc_final: 0.4368 (t60) outliers start: 52 outliers final: 32 residues processed: 424 average time/residue: 1.2968 time to fit residues: 615.1588 Evaluate side-chains 438 residues out of total 2183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 401 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 351 ARG Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain D residue 403 LYS Chi-restraints excluded: chain D residue 406 ARG Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 696 GLU Chi-restraints excluded: chain D residue 725 SER Chi-restraints excluded: chain D residue 748 GLN Chi-restraints excluded: chain D residue 890 GLU Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 944 GLU Chi-restraints excluded: chain D residue 965 THR Chi-restraints excluded: chain D residue 1072 LYS Chi-restraints excluded: chain D residue 1074 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1157 VAL Chi-restraints excluded: chain D residue 1204 SER Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain S residue 45 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.8268 > 50: distance: 59 - 61: 35.466 distance: 62 - 63: 56.325 distance: 62 - 65: 44.371 distance: 63 - 64: 39.456 distance: 63 - 67: 51.847 distance: 65 - 66: 35.934 distance: 67 - 68: 42.396 distance: 67 - 73: 55.099 distance: 68 - 69: 15.818 distance: 68 - 71: 47.414 distance: 69 - 70: 22.981 distance: 69 - 74: 34.020 distance: 71 - 72: 25.284 distance: 72 - 73: 58.361 distance: 74 - 75: 18.611 distance: 75 - 76: 14.282 distance: 75 - 78: 26.165 distance: 76 - 77: 14.852 distance: 76 - 82: 41.528 distance: 78 - 79: 45.276 distance: 79 - 80: 25.027 distance: 79 - 81: 49.764 distance: 82 - 83: 17.573 distance: 83 - 84: 24.869 distance: 83 - 86: 31.539 distance: 84 - 85: 39.502 distance: 84 - 91: 24.779 distance: 86 - 87: 33.497 distance: 87 - 88: 30.346 distance: 88 - 89: 9.983 distance: 89 - 90: 47.263 distance: 91 - 92: 42.930 distance: 92 - 93: 56.845 distance: 92 - 95: 54.174 distance: 93 - 94: 61.236 distance: 93 - 99: 46.924 distance: 95 - 96: 33.147 distance: 95 - 97: 29.942 distance: 96 - 98: 40.630 distance: 99 - 100: 42.029 distance: 100 - 101: 17.384 distance: 100 - 103: 17.578 distance: 101 - 102: 42.199 distance: 101 - 107: 21.898 distance: 103 - 104: 27.514 distance: 104 - 105: 38.894 distance: 104 - 106: 46.173 distance: 107 - 108: 31.861 distance: 108 - 109: 34.509 distance: 108 - 111: 16.552 distance: 109 - 110: 32.287 distance: 109 - 115: 52.742 distance: 111 - 112: 40.500 distance: 112 - 113: 28.726 distance: 112 - 114: 37.710 distance: 115 - 116: 35.935 distance: 116 - 117: 63.470 distance: 116 - 119: 66.827 distance: 117 - 118: 36.645 distance: 117 - 126: 56.931 distance: 119 - 120: 39.380 distance: 120 - 121: 41.242 distance: 121 - 122: 26.490 distance: 122 - 123: 43.966 distance: 123 - 124: 15.375 distance: 123 - 125: 20.585 distance: 126 - 127: 22.092 distance: 126 - 132: 41.315 distance: 127 - 128: 19.654 distance: 127 - 130: 20.640 distance: 128 - 129: 22.586 distance: 128 - 133: 32.534 distance: 130 - 131: 45.275 distance: 131 - 132: 42.063 distance: 133 - 134: 49.430 distance: 134 - 135: 47.251 distance: 134 - 137: 53.686 distance: 135 - 136: 49.618 distance: 135 - 140: 27.561 distance: 136 - 159: 30.011 distance: 137 - 138: 53.261 distance: 137 - 139: 21.510 distance: 143 - 163: 3.167