Starting phenix.real_space_refine on Fri Jan 24 05:14:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cud_7620/01_2025/6cud_7620_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cud_7620/01_2025/6cud_7620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6cud_7620/01_2025/6cud_7620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cud_7620/01_2025/6cud_7620.map" model { file = "/net/cci-nas-00/data/ceres_data/6cud_7620/01_2025/6cud_7620_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cud_7620/01_2025/6cud_7620_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.004 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 P 4 5.49 5 S 104 5.16 5 C 13844 2.51 5 N 3484 2.21 5 O 3592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 21028 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5196 Classifications: {'peptide': 704} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PTRANS': 22, 'TRANS': 681} Chain breaks: 2 Unresolved non-hydrogen bonds: 493 Unresolved non-hydrogen angles: 615 Unresolved non-hydrogen dihedrals: 380 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 3, 'ASN:plan1': 9, 'ASP:plan': 25, 'GLU:plan': 38, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 333 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'6OE': 1, 'FGJ': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, D Time building chain proxies: 12.75, per 1000 atoms: 0.61 Number of scatterers: 21028 At special positions: 0 Unit cell: (123.51, 123.51, 148.212, 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) S 104 16.00 P 4 15.00 O 3592 8.00 N 3484 7.00 C 13844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS A 184 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG A 903 " - " ASN A 404 " " NAG B 903 " - " ASN B 404 " " NAG C 903 " - " ASN C 404 " " NAG D 903 " - " ASN D 404 " Time building additional restraints: 5.33 Conformation dependent library (CDL) restraints added in 3.2 seconds 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5392 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 0 sheets defined 77.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 25 through 38 removed outlier: 3.953A pdb=" N ALA A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 50 removed outlier: 3.718A pdb=" N MET A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 50 " --> pdb=" O MET A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 72 removed outlier: 3.658A pdb=" N LEU A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 82 removed outlier: 3.633A pdb=" N LEU A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 100 Processing helix chain 'A' and resid 103 through 111 Processing helix chain 'A' and resid 112 through 117 removed outlier: 3.513A pdb=" N ALA A 116 " --> pdb=" O HIS A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 Processing helix chain 'A' and resid 160 through 171 removed outlier: 3.632A pdb=" N HIS A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 193 removed outlier: 3.746A pdb=" N HIS A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 210 removed outlier: 3.628A pdb=" N HIS A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 219 removed outlier: 4.516A pdb=" N SER A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 241 removed outlier: 3.920A pdb=" N THR A 225 " --> pdb=" O ASP A 221 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 264 removed outlier: 3.556A pdb=" N TYR A 247 " --> pdb=" O PHE A 243 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A 258 " --> pdb=" O CYS A 254 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 275 removed outlier: 3.717A pdb=" N VAL A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.956A pdb=" N LYS A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.683A pdb=" N VAL A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 removed outlier: 4.185A pdb=" N GLN A 317 " --> pdb=" O ASN A 313 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 321 " --> pdb=" O GLN A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 332 removed outlier: 4.132A pdb=" N GLU A 331 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN A 332 " --> pdb=" O LEU A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 328 through 332' Processing helix chain 'A' and resid 333 through 347 Processing helix chain 'A' and resid 350 through 357 removed outlier: 3.923A pdb=" N ILE A 357 " --> pdb=" O ILE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.629A pdb=" N LYS A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 392 Processing helix chain 'A' and resid 414 through 421 removed outlier: 4.445A pdb=" N LYS A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 448 removed outlier: 3.544A pdb=" N MET A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 428 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 455 removed outlier: 3.756A pdb=" N GLN A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 493 removed outlier: 3.812A pdb=" N VAL A 459 " --> pdb=" O GLN A 455 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA A 482 " --> pdb=" O ALA A 478 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 491 " --> pdb=" O GLN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.577A pdb=" N TYR A 509 " --> pdb=" O PRO A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 521 through 537 removed outlier: 3.523A pdb=" N VAL A 534 " --> pdb=" O TYR A 530 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 544 removed outlier: 3.967A pdb=" N ILE A 541 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 542 " --> pdb=" O SER A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 587 removed outlier: 3.779A pdb=" N GLN A 555 " --> pdb=" O PHE A 551 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 557 " --> pdb=" O PRO A 553 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE A 566 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYS A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 590 No H-bonds generated for 'chain 'A' and resid 588 through 590' Processing helix chain 'A' and resid 601 through 612 Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 618 through 622 removed outlier: 3.947A pdb=" N SER A 621 " --> pdb=" O GLU A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 665 removed outlier: 3.524A pdb=" N GLU A 632 " --> pdb=" O HIS A 628 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 647 " --> pdb=" O ASN A 643 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 661 " --> pdb=" O MET A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 686 removed outlier: 3.904A pdb=" N LYS A 679 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 786 removed outlier: 3.889A pdb=" N GLU A 786 " --> pdb=" O LYS A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 806 removed outlier: 3.929A pdb=" N GLU A 791 " --> pdb=" O VAL A 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 38 removed outlier: 3.953A pdb=" N ALA B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 50 removed outlier: 3.717A pdb=" N MET B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER B 50 " --> pdb=" O MET B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 72 removed outlier: 3.658A pdb=" N LEU B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 82 removed outlier: 3.634A pdb=" N LEU B 80 " --> pdb=" O GLU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 100 Processing helix chain 'B' and resid 103 through 111 Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.513A pdb=" N ALA B 116 " --> pdb=" O HIS B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 159 Processing helix chain 'B' and resid 160 through 171 removed outlier: 3.632A pdb=" N HIS B 165 " --> pdb=" O TYR B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 193 removed outlier: 3.745A pdb=" N HIS B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 210 removed outlier: 3.627A pdb=" N HIS B 198 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE B 203 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 removed outlier: 4.517A pdb=" N SER B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 241 removed outlier: 3.920A pdb=" N THR B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 239 " --> pdb=" O LYS B 235 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 264 removed outlier: 3.555A pdb=" N TYR B 247 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET B 252 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL B 258 " --> pdb=" O CYS B 254 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 275 removed outlier: 3.717A pdb=" N VAL B 271 " --> pdb=" O ASP B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.957A pdb=" N LYS B 302 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.683A pdb=" N VAL B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 323 removed outlier: 4.185A pdb=" N GLN B 317 " --> pdb=" O ASN B 313 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 321 " --> pdb=" O GLN B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 332 removed outlier: 4.131A pdb=" N GLU B 331 " --> pdb=" O GLY B 328 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN B 332 " --> pdb=" O LEU B 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 328 through 332' Processing helix chain 'B' and resid 333 through 347 Processing helix chain 'B' and resid 350 through 357 removed outlier: 3.924A pdb=" N ILE B 357 " --> pdb=" O ILE B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 361 through 366 removed outlier: 3.628A pdb=" N LYS B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 392 Processing helix chain 'B' and resid 414 through 421 removed outlier: 4.444A pdb=" N LYS B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR B 419 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 448 removed outlier: 3.544A pdb=" N MET B 427 " --> pdb=" O THR B 423 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 428 " --> pdb=" O TRP B 424 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 434 " --> pdb=" O MET B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 455 removed outlier: 3.755A pdb=" N GLN B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 493 removed outlier: 3.813A pdb=" N VAL B 459 " --> pdb=" O GLN B 455 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA B 482 " --> pdb=" O ALA B 478 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 491 " --> pdb=" O GLN B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 509 removed outlier: 3.577A pdb=" N TYR B 509 " --> pdb=" O PRO B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 512 No H-bonds generated for 'chain 'B' and resid 510 through 512' Processing helix chain 'B' and resid 521 through 537 removed outlier: 3.523A pdb=" N VAL B 534 " --> pdb=" O TYR B 530 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 535 " --> pdb=" O ALA B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 544 removed outlier: 3.967A pdb=" N ILE B 541 " --> pdb=" O PHE B 538 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B 542 " --> pdb=" O SER B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 587 removed outlier: 3.779A pdb=" N GLN B 555 " --> pdb=" O PHE B 551 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 556 " --> pdb=" O GLY B 552 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 557 " --> pdb=" O PRO B 553 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE B 566 " --> pdb=" O VAL B 562 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYS B 567 " --> pdb=" O LYS B 563 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 590 No H-bonds generated for 'chain 'B' and resid 588 through 590' Processing helix chain 'B' and resid 601 through 612 Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 618 through 622 removed outlier: 3.947A pdb=" N SER B 621 " --> pdb=" O GLU B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 665 removed outlier: 3.524A pdb=" N GLU B 632 " --> pdb=" O HIS B 628 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 647 " --> pdb=" O ASN B 643 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 685 removed outlier: 3.904A pdb=" N LYS B 679 " --> pdb=" O PHE B 675 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR B 684 " --> pdb=" O LEU B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 786 removed outlier: 3.888A pdb=" N GLU B 786 " --> pdb=" O LYS B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 806 removed outlier: 3.930A pdb=" N GLU B 791 " --> pdb=" O VAL B 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 38 removed outlier: 3.954A pdb=" N ALA C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 50 removed outlier: 3.718A pdb=" N MET C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER C 50 " --> pdb=" O MET C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 72 removed outlier: 3.657A pdb=" N LEU C 68 " --> pdb=" O ASN C 64 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 82 removed outlier: 3.634A pdb=" N LEU C 80 " --> pdb=" O GLU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 100 Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 112 through 117 removed outlier: 3.514A pdb=" N ALA C 116 " --> pdb=" O HIS C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 159 Processing helix chain 'C' and resid 160 through 171 removed outlier: 3.632A pdb=" N HIS C 165 " --> pdb=" O TYR C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 193 removed outlier: 3.746A pdb=" N HIS C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 210 removed outlier: 3.628A pdb=" N HIS C 198 " --> pdb=" O ASP C 194 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE C 203 " --> pdb=" O SER C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 removed outlier: 4.516A pdb=" N SER C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 241 removed outlier: 3.920A pdb=" N THR C 225 " --> pdb=" O ASP C 221 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS C 241 " --> pdb=" O ALA C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 264 removed outlier: 3.556A pdb=" N TYR C 247 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET C 252 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN C 253 " --> pdb=" O LYS C 249 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL C 258 " --> pdb=" O CYS C 254 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU C 264 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 275 removed outlier: 3.717A pdb=" N VAL C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.956A pdb=" N LYS C 302 " --> pdb=" O LYS C 298 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.683A pdb=" N VAL C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 323 removed outlier: 4.185A pdb=" N GLN C 317 " --> pdb=" O ASN C 313 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE C 321 " --> pdb=" O GLN C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 332 removed outlier: 4.133A pdb=" N GLU C 331 " --> pdb=" O GLY C 328 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN C 332 " --> pdb=" O LEU C 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 328 through 332' Processing helix chain 'C' and resid 333 through 347 Processing helix chain 'C' and resid 350 through 357 removed outlier: 3.924A pdb=" N ILE C 357 " --> pdb=" O ILE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 361 through 366 removed outlier: 3.628A pdb=" N LYS C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 392 Processing helix chain 'C' and resid 414 through 421 removed outlier: 4.444A pdb=" N LYS C 418 " --> pdb=" O ILE C 414 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR C 419 " --> pdb=" O PHE C 415 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR C 420 " --> pdb=" O ARG C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 448 removed outlier: 3.545A pdb=" N MET C 427 " --> pdb=" O THR C 423 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 428 " --> pdb=" O TRP C 424 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 434 " --> pdb=" O MET C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 455 removed outlier: 3.755A pdb=" N GLN C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 493 removed outlier: 3.813A pdb=" N VAL C 459 " --> pdb=" O GLN C 455 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA C 482 " --> pdb=" O ALA C 478 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C 491 " --> pdb=" O GLN C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 509 removed outlier: 3.578A pdb=" N TYR C 509 " --> pdb=" O PRO C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 512 No H-bonds generated for 'chain 'C' and resid 510 through 512' Processing helix chain 'C' and resid 521 through 537 removed outlier: 3.524A pdb=" N VAL C 534 " --> pdb=" O TYR C 530 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL C 535 " --> pdb=" O ALA C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 544 removed outlier: 3.967A pdb=" N ILE C 541 " --> pdb=" O PHE C 538 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 542 " --> pdb=" O SER C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 587 removed outlier: 3.779A pdb=" N GLN C 555 " --> pdb=" O PHE C 551 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 556 " --> pdb=" O GLY C 552 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER C 557 " --> pdb=" O PRO C 553 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE C 566 " --> pdb=" O VAL C 562 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYS C 567 " --> pdb=" O LYS C 563 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE C 568 " --> pdb=" O ASP C 564 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C 571 " --> pdb=" O LYS C 567 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 590 No H-bonds generated for 'chain 'C' and resid 588 through 590' Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 613 through 615 No H-bonds generated for 'chain 'C' and resid 613 through 615' Processing helix chain 'C' and resid 618 through 622 removed outlier: 3.947A pdb=" N SER C 621 " --> pdb=" O GLU C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 665 removed outlier: 3.524A pdb=" N GLU C 632 " --> pdb=" O HIS C 628 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL C 647 " --> pdb=" O ASN C 643 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER C 660 " --> pdb=" O ALA C 656 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER C 661 " --> pdb=" O MET C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 686 removed outlier: 3.904A pdb=" N LYS C 679 " --> pdb=" O PHE C 675 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR C 684 " --> pdb=" O LEU C 680 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP C 686 " --> pdb=" O LEU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 786 removed outlier: 3.889A pdb=" N GLU C 786 " --> pdb=" O LYS C 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 806 removed outlier: 3.929A pdb=" N GLU C 791 " --> pdb=" O VAL C 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 38 removed outlier: 3.953A pdb=" N ALA D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 50 removed outlier: 3.718A pdb=" N MET D 46 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER D 50 " --> pdb=" O MET D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.658A pdb=" N LEU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 82 removed outlier: 3.634A pdb=" N LEU D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 100 Processing helix chain 'D' and resid 103 through 111 Processing helix chain 'D' and resid 112 through 117 removed outlier: 3.514A pdb=" N ALA D 116 " --> pdb=" O HIS D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 159 Processing helix chain 'D' and resid 160 through 171 removed outlier: 3.632A pdb=" N HIS D 165 " --> pdb=" O TYR D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 193 removed outlier: 3.746A pdb=" N HIS D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 210 removed outlier: 3.627A pdb=" N HIS D 198 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE D 203 " --> pdb=" O SER D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 219 removed outlier: 4.516A pdb=" N SER D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 241 removed outlier: 3.921A pdb=" N THR D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 239 " --> pdb=" O LYS D 235 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS D 241 " --> pdb=" O ALA D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 264 removed outlier: 3.556A pdb=" N TYR D 247 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET D 252 " --> pdb=" O ARG D 248 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL D 258 " --> pdb=" O CYS D 254 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 275 removed outlier: 3.717A pdb=" N VAL D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 303 removed outlier: 3.956A pdb=" N LYS D 302 " --> pdb=" O LYS D 298 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.683A pdb=" N VAL D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 323 removed outlier: 4.185A pdb=" N GLN D 317 " --> pdb=" O ASN D 313 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE D 321 " --> pdb=" O GLN D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 332 removed outlier: 4.132A pdb=" N GLU D 331 " --> pdb=" O GLY D 328 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN D 332 " --> pdb=" O LEU D 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 328 through 332' Processing helix chain 'D' and resid 333 through 347 Processing helix chain 'D' and resid 350 through 357 removed outlier: 3.923A pdb=" N ILE D 357 " --> pdb=" O ILE D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 360 No H-bonds generated for 'chain 'D' and resid 358 through 360' Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.628A pdb=" N LYS D 365 " --> pdb=" O SER D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 392 Processing helix chain 'D' and resid 414 through 421 removed outlier: 4.444A pdb=" N LYS D 418 " --> pdb=" O ILE D 414 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR D 419 " --> pdb=" O PHE D 415 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 448 removed outlier: 3.544A pdb=" N MET D 427 " --> pdb=" O THR D 423 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 428 " --> pdb=" O TRP D 424 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 434 " --> pdb=" O MET D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 455 removed outlier: 3.756A pdb=" N GLN D 455 " --> pdb=" O GLU D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 493 removed outlier: 3.813A pdb=" N VAL D 459 " --> pdb=" O GLN D 455 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN D 481 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA D 482 " --> pdb=" O ALA D 478 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER D 491 " --> pdb=" O GLN D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 509 removed outlier: 3.578A pdb=" N TYR D 509 " --> pdb=" O PRO D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 512 No H-bonds generated for 'chain 'D' and resid 510 through 512' Processing helix chain 'D' and resid 521 through 537 removed outlier: 3.523A pdb=" N VAL D 534 " --> pdb=" O TYR D 530 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL D 535 " --> pdb=" O ALA D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 544 removed outlier: 3.967A pdb=" N ILE D 541 " --> pdb=" O PHE D 538 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA D 542 " --> pdb=" O SER D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 587 removed outlier: 3.779A pdb=" N GLN D 555 " --> pdb=" O PHE D 551 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 556 " --> pdb=" O GLY D 552 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER D 557 " --> pdb=" O PRO D 553 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE D 566 " --> pdb=" O VAL D 562 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYS D 567 " --> pdb=" O LYS D 563 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE D 568 " --> pdb=" O ASP D 564 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU D 571 " --> pdb=" O LYS D 567 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 590 No H-bonds generated for 'chain 'D' and resid 588 through 590' Processing helix chain 'D' and resid 601 through 612 Processing helix chain 'D' and resid 613 through 615 No H-bonds generated for 'chain 'D' and resid 613 through 615' Processing helix chain 'D' and resid 618 through 622 removed outlier: 3.947A pdb=" N SER D 621 " --> pdb=" O GLU D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 665 removed outlier: 3.524A pdb=" N GLU D 632 " --> pdb=" O HIS D 628 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL D 647 " --> pdb=" O ASN D 643 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER D 660 " --> pdb=" O ALA D 656 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER D 661 " --> pdb=" O MET D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 686 removed outlier: 3.904A pdb=" N LYS D 679 " --> pdb=" O PHE D 675 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR D 684 " --> pdb=" O LEU D 680 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP D 686 " --> pdb=" O LEU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 786 removed outlier: 3.888A pdb=" N GLU D 786 " --> pdb=" O LYS D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 806 removed outlier: 3.930A pdb=" N GLU D 791 " --> pdb=" O VAL D 787 " (cutoff:3.500A) 1284 hydrogen bonds defined for protein. 3816 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: 6.91 Time building geometry restraints manager: 5.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3334 1.32 - 1.45: 5818 1.45 - 1.57: 12168 1.57 - 1.69: 8 1.69 - 1.81: 176 Bond restraints: 21504 Sorted by residual: bond pdb=" C ILE C 40 " pdb=" N PRO C 41 " ideal model delta sigma weight residual 1.336 1.386 -0.050 1.20e-02 6.94e+03 1.73e+01 bond pdb=" C ILE D 40 " pdb=" N PRO D 41 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.68e+01 bond pdb=" C ILE A 40 " pdb=" N PRO A 41 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.68e+01 bond pdb=" C ILE B 40 " pdb=" N PRO B 41 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.67e+01 bond pdb=" N TYR C 410 " pdb=" CA TYR C 410 " ideal model delta sigma weight residual 1.453 1.489 -0.035 9.20e-03 1.18e+04 1.48e+01 ... (remaining 21499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 27711 2.31 - 4.63: 1401 4.63 - 6.94: 108 6.94 - 9.26: 48 9.26 - 11.57: 20 Bond angle restraints: 29288 Sorted by residual: angle pdb=" N LEU D 217 " pdb=" CA LEU D 217 " pdb=" C LEU D 217 " ideal model delta sigma weight residual 113.17 121.07 -7.90 1.26e+00 6.30e-01 3.93e+01 angle pdb=" N LEU B 217 " pdb=" CA LEU B 217 " pdb=" C LEU B 217 " ideal model delta sigma weight residual 113.17 121.07 -7.90 1.26e+00 6.30e-01 3.93e+01 angle pdb=" N LEU A 217 " pdb=" CA LEU A 217 " pdb=" C LEU A 217 " ideal model delta sigma weight residual 113.17 121.05 -7.88 1.26e+00 6.30e-01 3.91e+01 angle pdb=" N LEU C 217 " pdb=" CA LEU C 217 " pdb=" C LEU C 217 " ideal model delta sigma weight residual 113.17 121.01 -7.84 1.26e+00 6.30e-01 3.87e+01 angle pdb=" N SER D 216 " pdb=" CA SER D 216 " pdb=" C SER D 216 " ideal model delta sigma weight residual 111.36 117.42 -6.06 1.09e+00 8.42e-01 3.09e+01 ... (remaining 29283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.33: 12429 31.33 - 62.67: 226 62.67 - 94.00: 40 94.00 - 125.34: 0 125.34 - 156.67: 24 Dihedral angle restraints: 12719 sinusoidal: 4403 harmonic: 8316 Sorted by residual: dihedral pdb=" CD ARG A 540 " pdb=" NE ARG A 540 " pdb=" CZ ARG A 540 " pdb=" NH1 ARG A 540 " ideal model delta sinusoidal sigma weight residual 0.00 -67.50 67.50 1 1.00e+01 1.00e-02 5.93e+01 dihedral pdb=" CD ARG B 540 " pdb=" NE ARG B 540 " pdb=" CZ ARG B 540 " pdb=" NH1 ARG B 540 " ideal model delta sinusoidal sigma weight residual 0.00 -67.49 67.49 1 1.00e+01 1.00e-02 5.92e+01 dihedral pdb=" CD ARG D 540 " pdb=" NE ARG D 540 " pdb=" CZ ARG D 540 " pdb=" NH1 ARG D 540 " ideal model delta sinusoidal sigma weight residual 0.00 -67.45 67.45 1 1.00e+01 1.00e-02 5.92e+01 ... (remaining 12716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2636 0.060 - 0.121: 668 0.121 - 0.181: 133 0.181 - 0.241: 23 0.241 - 0.302: 16 Chirality restraints: 3476 Sorted by residual: chirality pdb=" CA SER B 218 " pdb=" N SER B 218 " pdb=" C SER B 218 " pdb=" CB SER B 218 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA SER A 218 " pdb=" N SER A 218 " pdb=" C SER A 218 " pdb=" CB SER A 218 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA SER C 218 " pdb=" N SER C 218 " pdb=" C SER C 218 " pdb=" CB SER C 218 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 3473 not shown) Planarity restraints: 3620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 540 " -1.013 9.50e-02 1.11e+02 4.54e-01 1.25e+02 pdb=" NE ARG B 540 " 0.061 2.00e-02 2.50e+03 pdb=" CZ ARG B 540 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 540 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 540 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 540 " -1.013 9.50e-02 1.11e+02 4.54e-01 1.24e+02 pdb=" NE ARG C 540 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG C 540 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 540 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 540 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 540 " -1.013 9.50e-02 1.11e+02 4.54e-01 1.24e+02 pdb=" NE ARG A 540 " 0.061 2.00e-02 2.50e+03 pdb=" CZ ARG A 540 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 540 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 540 " -0.023 2.00e-02 2.50e+03 ... (remaining 3617 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 132 2.62 - 3.19: 17724 3.19 - 3.76: 30575 3.76 - 4.33: 39755 4.33 - 4.90: 66459 Nonbonded interactions: 154645 Sorted by model distance: nonbonded pdb=" SG CYS B 182 " pdb=" SG CYS B 184 " model vdw 2.049 3.760 nonbonded pdb=" SG CYS D 182 " pdb=" SG CYS D 184 " model vdw 2.049 3.760 nonbonded pdb=" SG CYS C 182 " pdb=" SG CYS C 184 " model vdw 2.050 3.760 nonbonded pdb=" OD1 ASP B 92 " pdb=" NH2 ARG B 144 " model vdw 2.171 3.120 nonbonded pdb=" OD1 ASP A 92 " pdb=" NH2 ARG A 144 " model vdw 2.172 3.120 ... (remaining 154640 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.640 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: 0.880 Check model and map are aligned: 0.170 Set scattering table: 0.240 Process input model: 45.860 Find NCS groups from input model: 0.490 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.007 0.059 21504 Z= 0.443 Angle : 1.135 11.573 29288 Z= 0.705 Chirality : 0.059 0.302 3476 Planarity : 0.017 0.454 3616 Dihedral : 14.710 156.670 7324 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.37 % Favored : 95.49 % Rotamer: Outliers : 1.47 % Allowed : 5.53 % Favored : 93.00 % 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: -3.04 (0.13), residues: 2792 helix: -1.63 (0.10), residues: 1948 sheet: None (None), residues: 0 loop : -2.59 (0.17), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 611 HIS 0.006 0.002 HIS C 377 PHE 0.031 0.002 PHE D 538 TYR 0.035 0.002 TYR B 636 ARG 0.007 0.001 ARG B 677 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 ASP cc_start: 0.7747 (m-30) cc_final: 0.7520 (m-30) REVERT: A 351 LEU cc_start: 0.7410 (mt) cc_final: 0.7055 (mt) REVERT: A 410 TYR cc_start: 0.5312 (OUTLIER) cc_final: 0.4272 (p90) REVERT: A 430 MET cc_start: 0.8349 (mmm) cc_final: 0.8100 (tpp) REVERT: A 521 ASP cc_start: 0.7881 (t0) cc_final: 0.7573 (t0) REVERT: B 246 ASP cc_start: 0.7717 (m-30) cc_final: 0.7506 (m-30) REVERT: B 351 LEU cc_start: 0.7448 (mt) cc_final: 0.7090 (mt) REVERT: B 410 TYR cc_start: 0.5533 (OUTLIER) cc_final: 0.4312 (p90) REVERT: B 430 MET cc_start: 0.8350 (mmm) cc_final: 0.8066 (tpp) REVERT: B 521 ASP cc_start: 0.8044 (t0) cc_final: 0.7662 (t0) REVERT: C 246 ASP cc_start: 0.7762 (m-30) cc_final: 0.7550 (m-30) REVERT: C 351 LEU cc_start: 0.7416 (mt) cc_final: 0.7051 (mt) REVERT: C 410 TYR cc_start: 0.5315 (OUTLIER) cc_final: 0.4327 (p90) REVERT: C 430 MET cc_start: 0.8352 (mmm) cc_final: 0.8093 (tpp) REVERT: C 521 ASP cc_start: 0.7909 (t0) cc_final: 0.7620 (t0) REVERT: D 351 LEU cc_start: 0.7426 (mt) cc_final: 0.7069 (mt) REVERT: D 410 TYR cc_start: 0.5433 (OUTLIER) cc_final: 0.4347 (p90) REVERT: D 430 MET cc_start: 0.8367 (mmm) cc_final: 0.8094 (tpp) REVERT: D 521 ASP cc_start: 0.7882 (t0) cc_final: 0.7569 (t0) outliers start: 28 outliers final: 12 residues processed: 233 average time/residue: 0.3183 time to fit residues: 117.1238 Evaluate side-chains 171 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 445 TRP Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 410 TYR Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 445 TRP Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 410 TYR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 445 TRP Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 410 TYR Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 445 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 0.3980 chunk 212 optimal weight: 0.1980 chunk 117 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 219 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 133 optimal weight: 7.9990 chunk 163 optimal weight: 0.6980 chunk 254 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS A 198 HIS B 112 HIS B 198 HIS C 112 HIS C 198 HIS D 112 HIS D 198 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.099168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.074223 restraints weight = 47015.389| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.92 r_work: 0.2943 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21504 Z= 0.177 Angle : 0.573 9.455 29288 Z= 0.301 Chirality : 0.038 0.126 3476 Planarity : 0.004 0.044 3616 Dihedral : 14.975 154.963 3296 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.83 % Favored : 96.02 % Rotamer: Outliers : 1.16 % Allowed : 8.74 % Favored : 90.11 % 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: -0.59 (0.15), residues: 2792 helix: 0.37 (0.12), residues: 1952 sheet: None (None), residues: 0 loop : -2.13 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 673 HIS 0.003 0.001 HIS A 628 PHE 0.018 0.001 PHE A 181 TYR 0.017 0.002 TYR B 488 ARG 0.007 0.000 ARG C 330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 2.258 Fit side-chains REVERT: A 351 LEU cc_start: 0.7132 (mt) cc_final: 0.6805 (mt) REVERT: A 445 TRP cc_start: 0.6532 (OUTLIER) cc_final: 0.6181 (t-100) REVERT: B 351 LEU cc_start: 0.7223 (mt) cc_final: 0.6901 (mt) REVERT: B 430 MET cc_start: 0.8414 (mmm) cc_final: 0.8213 (tpp) REVERT: B 445 TRP cc_start: 0.6530 (OUTLIER) cc_final: 0.6150 (t-100) REVERT: C 351 LEU cc_start: 0.7106 (mt) cc_final: 0.6773 (mt) REVERT: C 445 TRP cc_start: 0.6423 (OUTLIER) cc_final: 0.6048 (t-100) REVERT: D 351 LEU cc_start: 0.7107 (mt) cc_final: 0.6776 (mt) REVERT: D 445 TRP cc_start: 0.6407 (OUTLIER) cc_final: 0.6036 (t-100) REVERT: D 521 ASP cc_start: 0.7866 (t0) cc_final: 0.7643 (t0) REVERT: D 583 MET cc_start: 0.9059 (mmm) cc_final: 0.8818 (mmt) outliers start: 22 outliers final: 18 residues processed: 195 average time/residue: 0.2986 time to fit residues: 95.3471 Evaluate side-chains 176 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 445 TRP Chi-restraints excluded: chain A residue 452 TYR Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 445 TRP Chi-restraints excluded: chain B residue 452 TYR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 445 TRP Chi-restraints excluded: chain C residue 452 TYR Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 445 TRP Chi-restraints excluded: chain D residue 452 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 52 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 201 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 194 optimal weight: 0.5980 chunk 142 optimal weight: 0.3980 chunk 193 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.099945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.074968 restraints weight = 46596.077| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.91 r_work: 0.2954 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 21504 Z= 0.154 Angle : 0.513 9.758 29288 Z= 0.260 Chirality : 0.038 0.119 3476 Planarity : 0.004 0.038 3616 Dihedral : 13.938 154.581 3288 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.76 % Favored : 96.10 % Rotamer: Outliers : 2.11 % Allowed : 10.21 % Favored : 87.68 % 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: 0.62 (0.16), residues: 2792 helix: 1.39 (0.12), residues: 1964 sheet: None (None), residues: 0 loop : -2.04 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 356 HIS 0.002 0.001 HIS A 198 PHE 0.013 0.001 PHE C 181 TYR 0.017 0.001 TYR B 636 ARG 0.006 0.000 ARG C 330 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 2.246 Fit side-chains REVERT: A 351 LEU cc_start: 0.7262 (mt) cc_final: 0.6937 (mt) REVERT: A 572 PHE cc_start: 0.8343 (t80) cc_final: 0.8066 (t80) REVERT: A 583 MET cc_start: 0.9039 (mmt) cc_final: 0.8733 (mmt) REVERT: B 194 ASP cc_start: 0.8111 (t0) cc_final: 0.7824 (t70) REVERT: B 351 LEU cc_start: 0.7157 (mt) cc_final: 0.6840 (mt) REVERT: C 351 LEU cc_start: 0.7298 (mt) cc_final: 0.6974 (mt) REVERT: C 572 PHE cc_start: 0.8330 (t80) cc_final: 0.8080 (t80) REVERT: C 583 MET cc_start: 0.9033 (mmt) cc_final: 0.8706 (mmt) REVERT: D 351 LEU cc_start: 0.7274 (mt) cc_final: 0.6940 (mt) REVERT: D 572 PHE cc_start: 0.8307 (t80) cc_final: 0.8040 (t80) outliers start: 40 outliers final: 22 residues processed: 203 average time/residue: 0.2566 time to fit residues: 90.2578 Evaluate side-chains 179 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 452 TYR Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain D residue 181 PHE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 550 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.7899 > 50: distance: 12 - 31: 19.488 distance: 17 - 36: 22.951 distance: 20 - 24: 8.126 distance: 21 - 41: 31.356 distance: 24 - 25: 13.090 distance: 25 - 26: 19.312 distance: 25 - 28: 24.516 distance: 26 - 27: 13.465 distance: 26 - 31: 15.345 distance: 27 - 49: 27.871 distance: 28 - 29: 9.186 distance: 28 - 30: 11.223 distance: 31 - 32: 18.722 distance: 32 - 33: 41.798 distance: 32 - 35: 15.142 distance: 33 - 34: 11.794 distance: 33 - 36: 48.223 distance: 36 - 37: 15.909 distance: 37 - 38: 17.113 distance: 37 - 40: 14.038 distance: 38 - 39: 19.567 distance: 38 - 41: 15.462 distance: 41 - 42: 17.885 distance: 42 - 43: 14.641 distance: 42 - 45: 26.802 distance: 43 - 44: 10.826 distance: 43 - 49: 8.405 distance: 45 - 46: 7.300 distance: 45 - 47: 8.311 distance: 49 - 50: 7.870 distance: 50 - 51: 12.069 distance: 50 - 53: 5.961 distance: 51 - 52: 16.016 distance: 51 - 57: 8.652 distance: 54 - 55: 17.131 distance: 54 - 56: 13.724 distance: 57 - 58: 3.269 distance: 58 - 59: 16.457 distance: 58 - 61: 15.720 distance: 59 - 60: 9.617 distance: 59 - 65: 13.269 distance: 61 - 62: 9.655 distance: 62 - 63: 15.280 distance: 62 - 64: 14.700 distance: 65 - 66: 15.262 distance: 66 - 67: 24.076 distance: 67 - 68: 29.348 distance: 67 - 69: 12.157 distance: 69 - 70: 14.971 distance: 70 - 71: 12.650 distance: 70 - 73: 13.447 distance: 71 - 72: 15.465 distance: 71 - 74: 11.695 distance: 75 - 76: 6.542 distance: 75 - 78: 5.800 distance: 76 - 77: 16.265 distance: 76 - 82: 14.196 distance: 78 - 79: 4.300 distance: 79 - 81: 3.184 distance: 82 - 83: 5.424 distance: 83 - 84: 4.429 distance: 83 - 86: 8.320 distance: 84 - 85: 3.282