Starting phenix.real_space_refine on Sun Sep 29 10:32:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdm_9100/09_2024/6mdm_9100_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdm_9100/09_2024/6mdm_9100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdm_9100/09_2024/6mdm_9100.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdm_9100/09_2024/6mdm_9100.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdm_9100/09_2024/6mdm_9100_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdm_9100/09_2024/6mdm_9100_trim.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 31 5.49 5 S 210 5.16 5 C 22976 2.51 5 N 6342 2.21 5 O 7008 1.98 5 H 36604 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "A ARG 388": not complete - not flipped Time to flip 50 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 73171 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 11004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 11004 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 29, 'TRANS': 669} Chain breaks: 3 Chain: "B" Number of atoms: 11079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 11079 Classifications: {'peptide': 704} Link IDs: {'PTRANS': 29, 'TRANS': 674} Chain breaks: 3 Chain: "C" Number of atoms: 11164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 11164 Classifications: {'peptide': 709} Link IDs: {'PTRANS': 29, 'TRANS': 679} Chain breaks: 3 Chain: "D" Number of atoms: 11232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 11232 Classifications: {'peptide': 713} Link IDs: {'PTRANS': 29, 'TRANS': 683} Chain breaks: 3 Chain: "E" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 8130 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 21, 'TRANS': 492} Chain breaks: 2 Chain: "F" Number of atoms: 7007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 7007 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 20, 'TRANS': 445} Chain breaks: 5 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 73 Chain: "H" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2301 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'TRANS': 146} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1060 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "J" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 984 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'TRANS': 60} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 4430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4430 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 3, 'TRANS': 282} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4447 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 3, 'TRANS': 282} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 25.58, per 1000 atoms: 0.35 Number of scatterers: 73171 At special positions: 0 Unit cell: (149.34, 148.03, 221.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 210 16.00 P 31 15.00 O 7008 8.00 N 6342 7.00 C 22976 6.00 H 36604 1.00 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 - 3.00 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 Time building additional restraints: 14.30 Conformation dependent library (CDL) restraints added in 4.6 seconds 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8688 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 35 sheets defined 51.7% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.59 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 removed outlier: 3.993A pdb=" N LEU A 18 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 114 through 125 removed outlier: 3.607A pdb=" N ILE A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 removed outlier: 3.836A pdb=" N PHE A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 249 removed outlier: 3.697A pdb=" N VAL A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLN A 247 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.619A pdb=" N ARG A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 317 removed outlier: 4.180A pdb=" N ALA A 300 " --> pdb=" O GLY A 296 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ILE A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU A 305 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 360 removed outlier: 4.262A pdb=" N GLN A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 418 removed outlier: 4.454A pdb=" N ARG A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N MET A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 432 removed outlier: 3.518A pdb=" N LEU A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 456 removed outlier: 4.018A pdb=" N GLU A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N MET A 453 " --> pdb=" O GLN A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 486 Processing helix chain 'A' and resid 498 through 503 removed outlier: 3.887A pdb=" N TYR A 502 " --> pdb=" O ASP A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 530 removed outlier: 3.709A pdb=" N THR A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 560 removed outlier: 4.354A pdb=" N SER A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 574 Processing helix chain 'A' and resid 577 through 594 removed outlier: 3.819A pdb=" N CYS A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 removed outlier: 3.672A pdb=" N LEU A 608 " --> pdb=" O ASP A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 632 removed outlier: 3.624A pdb=" N LEU A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 655 Processing helix chain 'A' and resid 672 through 684 removed outlier: 3.732A pdb=" N GLU A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 698 removed outlier: 3.710A pdb=" N ILE A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 719 removed outlier: 3.671A pdb=" N GLN A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 734 removed outlier: 4.409A pdb=" N VAL A 726 " --> pdb=" O PRO A 722 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ARG A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 19 Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 114 through 125 Processing helix chain 'B' and resid 223 through 240 removed outlier: 5.626A pdb=" N SER B 237 " --> pdb=" O ARG B 233 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ARG B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 249 removed outlier: 3.524A pdb=" N VAL B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 277 Processing helix chain 'B' and resid 296 through 316 removed outlier: 4.446A pdb=" N ILE B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU B 305 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASP B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 removed outlier: 4.423A pdb=" N ILE B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 359 removed outlier: 3.584A pdb=" N ASP B 359 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.585A pdb=" N LEU B 378 " --> pdb=" O ARG B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.540A pdb=" N LEU B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 385 " --> pdb=" O GLU B 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 380 through 385' Processing helix chain 'B' and resid 399 through 417 removed outlier: 3.652A pdb=" N LEU B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG B 413 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N MET B 414 " --> pdb=" O HIS B 410 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N HIS B 417 " --> pdb=" O ARG B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 433 removed outlier: 3.543A pdb=" N LEU B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 455 Processing helix chain 'B' and resid 481 through 486 removed outlier: 3.529A pdb=" N GLU B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 502 removed outlier: 3.923A pdb=" N SER B 501 " --> pdb=" O ASP B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 530 removed outlier: 4.050A pdb=" N THR B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 560 removed outlier: 3.520A pdb=" N LEU B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 593 removed outlier: 3.688A pdb=" N ALA B 584 " --> pdb=" O ALA B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 609 Processing helix chain 'B' and resid 619 through 630 Processing helix chain 'B' and resid 649 through 655 Processing helix chain 'B' and resid 673 through 684 removed outlier: 3.541A pdb=" N ALA B 679 " --> pdb=" O GLN B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 698 Processing helix chain 'B' and resid 706 through 719 removed outlier: 4.186A pdb=" N MET B 712 " --> pdb=" O LYS B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 735 removed outlier: 4.366A pdb=" N VAL B 726 " --> pdb=" O PRO B 722 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG B 727 " --> pdb=" O GLU B 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 19 Processing helix chain 'C' and resid 63 through 71 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 103 through 107 removed outlier: 4.131A pdb=" N ILE C 107 " --> pdb=" O LYS C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 125 removed outlier: 3.815A pdb=" N ALA C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 201 removed outlier: 3.803A pdb=" N LYS C 200 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 236 removed outlier: 3.688A pdb=" N SER C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 249 removed outlier: 3.642A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 276 removed outlier: 3.523A pdb=" N LEU C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 317 removed outlier: 3.805A pdb=" N ILE C 302 " --> pdb=" O SER C 298 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG C 303 " --> pdb=" O GLU C 299 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU C 311 " --> pdb=" O ALA C 307 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 359 removed outlier: 4.428A pdb=" N VAL C 351 " --> pdb=" O HIS C 347 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN C 352 " --> pdb=" O ASP C 348 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER C 356 " --> pdb=" O ASN C 352 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP C 359 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 Processing helix chain 'C' and resid 380 through 385 Processing helix chain 'C' and resid 399 through 417 removed outlier: 3.906A pdb=" N GLN C 405 " --> pdb=" O LYS C 401 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N MET C 414 " --> pdb=" O HIS C 410 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS C 417 " --> pdb=" O ARG C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 433 removed outlier: 3.710A pdb=" N LEU C 429 " --> pdb=" O ASP C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 457 removed outlier: 3.833A pdb=" N GLY C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN C 449 " --> pdb=" O VAL C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 486 Processing helix chain 'C' and resid 497 through 503 removed outlier: 4.323A pdb=" N SER C 501 " --> pdb=" O GLU C 497 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR C 502 " --> pdb=" O ASP C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 531 removed outlier: 3.717A pdb=" N THR C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 561 removed outlier: 3.572A pdb=" N ALA C 557 " --> pdb=" O ALA C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 593 Processing helix chain 'C' and resid 604 through 609 Processing helix chain 'C' and resid 619 through 632 removed outlier: 3.653A pdb=" N LEU C 623 " --> pdb=" O SER C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 655 Processing helix chain 'C' and resid 672 through 684 Processing helix chain 'C' and resid 690 through 699 Processing helix chain 'C' and resid 706 through 719 removed outlier: 4.112A pdb=" N MET C 712 " --> pdb=" O LYS C 708 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLU C 715 " --> pdb=" O LEU C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 738 removed outlier: 4.562A pdb=" N VAL C 726 " --> pdb=" O PRO C 722 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ARG C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU C 735 " --> pdb=" O ALA C 731 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU C 736 " --> pdb=" O LEU C 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 19 removed outlier: 3.519A pdb=" N LEU D 18 " --> pdb=" O GLU D 15 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER D 19 " --> pdb=" O LEU D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 71 Processing helix chain 'D' and resid 114 through 125 removed outlier: 3.852A pdb=" N ILE D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 235 Processing helix chain 'D' and resid 235 through 240 Processing helix chain 'D' and resid 242 through 248 Processing helix chain 'D' and resid 265 through 276 removed outlier: 3.758A pdb=" N LEU D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLY D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 316 removed outlier: 4.087A pdb=" N LYS D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU D 305 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ASP D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 334 removed outlier: 4.511A pdb=" N ILE D 333 " --> pdb=" O GLU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 348 removed outlier: 4.059A pdb=" N ASP D 348 " --> pdb=" O GLY D 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 345 through 348' Processing helix chain 'D' and resid 349 through 359 removed outlier: 3.909A pdb=" N GLN D 353 " --> pdb=" O THR D 349 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASP D 359 " --> pdb=" O LEU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 384 Processing helix chain 'D' and resid 401 through 417 removed outlier: 3.800A pdb=" N GLN D 405 " --> pdb=" O LYS D 401 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N HIS D 410 " --> pdb=" O ILE D 406 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ARG D 413 " --> pdb=" O ILE D 409 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N MET D 414 " --> pdb=" O HIS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 433 Processing helix chain 'D' and resid 438 through 458 removed outlier: 4.241A pdb=" N LEU D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG D 455 " --> pdb=" O THR D 451 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N HIS D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 489 Processing helix chain 'D' and resid 511 through 531 removed outlier: 4.025A pdb=" N THR D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN D 526 " --> pdb=" O GLU D 522 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN D 527 " --> pdb=" O LEU D 523 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR D 528 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 Processing helix chain 'D' and resid 577 through 594 removed outlier: 3.992A pdb=" N MET D 585 " --> pdb=" O LYS D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 609 Processing helix chain 'D' and resid 619 through 631 removed outlier: 4.073A pdb=" N LEU D 623 " --> pdb=" O SER D 619 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS D 631 " --> pdb=" O LEU D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 655 removed outlier: 3.537A pdb=" N GLU D 654 " --> pdb=" O VAL D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 684 Processing helix chain 'D' and resid 687 through 699 removed outlier: 5.301A pdb=" N GLN D 697 " --> pdb=" O THR D 693 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D 698 " --> pdb=" O ILE D 694 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS D 699 " --> pdb=" O ALA D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 719 removed outlier: 4.138A pdb=" N MET D 712 " --> pdb=" O LYS D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 737 removed outlier: 4.493A pdb=" N VAL D 726 " --> pdb=" O PRO D 722 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU D 735 " --> pdb=" O ALA D 731 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 220 removed outlier: 4.296A pdb=" N GLY E 219 " --> pdb=" O GLU E 216 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE E 220 " --> pdb=" O LYS E 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 216 through 220' Processing helix chain 'E' and resid 223 through 236 removed outlier: 3.899A pdb=" N PHE E 227 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 277 Processing helix chain 'E' and resid 286 through 291 removed outlier: 4.488A pdb=" N ILE E 290 " --> pdb=" O GLY E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 317 removed outlier: 4.052A pdb=" N ILE E 302 " --> pdb=" O SER E 298 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG E 303 " --> pdb=" O GLU E 299 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU E 305 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP E 308 " --> pdb=" O LYS E 304 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA E 309 " --> pdb=" O LEU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 334 removed outlier: 3.739A pdb=" N ILE E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 360 Processing helix chain 'E' and resid 376 through 384 removed outlier: 4.640A pdb=" N GLU E 381 " --> pdb=" O ASP E 377 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ALA E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU E 383 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU E 384 " --> pdb=" O ASP E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 416 removed outlier: 4.253A pdb=" N ARG E 413 " --> pdb=" O ILE E 409 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N MET E 414 " --> pdb=" O HIS E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 433 removed outlier: 4.312A pdb=" N VAL E 431 " --> pdb=" O LYS E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 455 removed outlier: 3.509A pdb=" N VAL E 445 " --> pdb=" O LEU E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 489 removed outlier: 3.961A pdb=" N ILE E 488 " --> pdb=" O LEU E 484 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS E 489 " --> pdb=" O GLU E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 531 removed outlier: 4.120A pdb=" N THR E 515 " --> pdb=" O GLY E 511 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 561 Processing helix chain 'E' and resid 569 through 574 removed outlier: 3.683A pdb=" N ILE E 574 " --> pdb=" O ASP E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 595 removed outlier: 3.756A pdb=" N MET E 585 " --> pdb=" O LYS E 581 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS E 587 " --> pdb=" O GLN E 583 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE E 588 " --> pdb=" O ALA E 584 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER E 595 " --> pdb=" O ASP E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 609 Processing helix chain 'E' and resid 619 through 632 removed outlier: 3.595A pdb=" N LEU E 623 " --> pdb=" O SER E 619 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU E 629 " --> pdb=" O ALA E 625 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 630 " --> pdb=" O LEU E 626 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS E 631 " --> pdb=" O LEU E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 655 Processing helix chain 'E' and resid 672 through 684 Processing helix chain 'E' and resid 687 through 699 removed outlier: 3.673A pdb=" N GLN E 696 " --> pdb=" O THR E 692 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLN E 697 " --> pdb=" O THR E 693 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS E 699 " --> pdb=" O ALA E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 719 removed outlier: 3.733A pdb=" N GLU E 715 " --> pdb=" O LEU E 711 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN E 719 " --> pdb=" O GLU E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 734 removed outlier: 4.006A pdb=" N ALA E 731 " --> pdb=" O ARG E 727 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 239 removed outlier: 3.520A pdb=" N PHE F 231 " --> pdb=" O PHE F 227 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG F 232 " --> pdb=" O SER F 228 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG F 233 " --> pdb=" O ASP F 229 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA F 234 " --> pdb=" O ILE F 230 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER F 237 " --> pdb=" O ARG F 233 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG F 238 " --> pdb=" O ALA F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 278 removed outlier: 3.502A pdb=" N ASN F 278 " --> pdb=" O GLY F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 316 removed outlier: 4.088A pdb=" N PHE F 306 " --> pdb=" O ILE F 302 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA F 309 " --> pdb=" O LEU F 305 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU F 312 " --> pdb=" O ASP F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 359 Processing helix chain 'F' and resid 399 through 411 Processing helix chain 'F' and resid 427 through 432 Processing helix chain 'F' and resid 433 through 436 Processing helix chain 'F' and resid 443 through 454 removed outlier: 4.774A pdb=" N GLN F 449 " --> pdb=" O VAL F 445 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N SER F 450 " --> pdb=" O ARG F 446 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ALA F 452 " --> pdb=" O ALA F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 503 removed outlier: 3.650A pdb=" N TYR F 502 " --> pdb=" O TYR F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 530 removed outlier: 3.886A pdb=" N LEU F 524 " --> pdb=" O ASP F 520 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS F 529 " --> pdb=" O VAL F 525 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN F 530 " --> pdb=" O GLN F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 549 through 560 Processing helix chain 'F' and resid 577 through 595 removed outlier: 3.553A pdb=" N GLN F 583 " --> pdb=" O THR F 579 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP F 591 " --> pdb=" O LYS F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 609 Processing helix chain 'F' and resid 619 through 632 removed outlier: 3.641A pdb=" N LEU F 623 " --> pdb=" O SER F 619 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS F 631 " --> pdb=" O LEU F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 655 Processing helix chain 'F' and resid 672 through 684 Processing helix chain 'F' and resid 687 through 696 removed outlier: 3.888A pdb=" N THR F 693 " --> pdb=" O LYS F 689 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE F 694 " --> pdb=" O GLU F 690 " (cutoff:3.500A) Processing helix chain 'F' and resid 706 through 720 removed outlier: 4.074A pdb=" N GLU F 715 " --> pdb=" O LEU F 711 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET F 716 " --> pdb=" O MET F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 736 Processing helix chain 'H' and resid 19 through 22 removed outlier: 3.576A pdb=" N ALA H 22 " --> pdb=" O ASP H 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 19 through 22' Processing helix chain 'H' and resid 23 through 35 Processing helix chain 'H' and resid 36 through 72 removed outlier: 3.763A pdb=" N LYS H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG H 45 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N HIS H 66 " --> pdb=" O GLU H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 83 removed outlier: 4.280A pdb=" N LYS H 83 " --> pdb=" O LYS H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 201 removed outlier: 3.561A pdb=" N GLY H 158 " --> pdb=" O SER H 154 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU H 183 " --> pdb=" O ASP H 179 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP H 193 " --> pdb=" O LYS H 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 237 removed outlier: 4.270A pdb=" N ILE I 202 " --> pdb=" O ARG I 198 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU I 228 " --> pdb=" O GLU I 224 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET I 229 " --> pdb=" O SER I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 252 removed outlier: 4.214A pdb=" N ARG I 246 " --> pdb=" O ASP I 242 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP I 250 " --> pdb=" O ARG I 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 86 removed outlier: 3.640A pdb=" N GLN J 34 " --> pdb=" O ARG J 30 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU J 54 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU J 55 " --> pdb=" O ASP J 51 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS J 59 " --> pdb=" O GLU J 55 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP J 64 " --> pdb=" O LEU J 60 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA J 69 " --> pdb=" O ASP J 65 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA J 72 " --> pdb=" O ASP J 68 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY J 73 " --> pdb=" O ALA J 69 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE J 77 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU J 78 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR J 79 " --> pdb=" O SER J 75 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG J 86 " --> pdb=" O ALA J 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 19 removed outlier: 3.631A pdb=" N ARG K 19 " --> pdb=" O ALA K 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 55 Processing helix chain 'K' and resid 57 through 72 Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 80 through 95 removed outlier: 3.841A pdb=" N PHE K 92 " --> pdb=" O ALA K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 114 removed outlier: 3.794A pdb=" N GLU K 109 " --> pdb=" O MET K 105 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE K 110 " --> pdb=" O ARG K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 134 removed outlier: 3.543A pdb=" N ALA K 121 " --> pdb=" O PHE K 117 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 154 removed outlier: 4.155A pdb=" N ALA K 143 " --> pdb=" O GLU K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 176 removed outlier: 3.878A pdb=" N LEU K 165 " --> pdb=" O ALA K 161 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR K 171 " --> pdb=" O LYS K 167 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN K 174 " --> pdb=" O GLY K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 195 removed outlier: 3.828A pdb=" N ILE K 182 " --> pdb=" O TYR K 178 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER K 191 " --> pdb=" O GLN K 187 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER K 195 " --> pdb=" O SER K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 212 removed outlier: 3.602A pdb=" N CYS K 212 " --> pdb=" O LYS K 208 " (cutoff:3.500A) Processing helix chain 'K' and resid 219 through 226 Processing helix chain 'K' and resid 234 through 238 Processing helix chain 'K' and resid 241 through 253 removed outlier: 4.605A pdb=" N GLU K 249 " --> pdb=" O LYS K 245 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 270 removed outlier: 3.878A pdb=" N VAL K 263 " --> pdb=" O TYR K 259 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER K 268 " --> pdb=" O LYS K 264 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE K 269 " --> pdb=" O GLU K 265 " (cutoff:3.500A) Processing helix chain 'K' and resid 273 through 291 Processing helix chain 'L' and resid 10 through 21 removed outlier: 3.581A pdb=" N ALA L 15 " --> pdb=" O MET L 11 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS L 20 " --> pdb=" O GLU L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 55 removed outlier: 3.699A pdb=" N LYS L 53 " --> pdb=" O ALA L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 74 removed outlier: 3.642A pdb=" N HIS L 72 " --> pdb=" O ALA L 68 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN L 74 " --> pdb=" O GLN L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 93 removed outlier: 3.527A pdb=" N PHE L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS L 93 " --> pdb=" O GLY L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 115 removed outlier: 3.936A pdb=" N ASN L 102 " --> pdb=" O GLN L 98 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP L 113 " --> pdb=" O GLU L 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 134 removed outlier: 3.547A pdb=" N ILE L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER L 126 " --> pdb=" O LYS L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 155 Processing helix chain 'L' and resid 157 through 170 removed outlier: 3.659A pdb=" N ALA L 161 " --> pdb=" O SER L 157 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS L 167 " --> pdb=" O LYS L 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 173 No H-bonds generated for 'chain 'L' and resid 171 through 173' Processing helix chain 'L' and resid 177 through 190 removed outlier: 3.500A pdb=" N ASP L 183 " --> pdb=" O GLN L 179 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE L 184 " --> pdb=" O LYS L 180 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR L 185 " --> pdb=" O ALA L 181 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU L 186 " --> pdb=" O ILE L 182 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLN L 187 " --> pdb=" O ASP L 183 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL L 188 " --> pdb=" O ILE L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 209 removed outlier: 3.801A pdb=" N LYS L 203 " --> pdb=" O LYS L 199 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASP L 204 " --> pdb=" O TYR L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 228 Processing helix chain 'L' and resid 240 through 254 removed outlier: 3.558A pdb=" N ALA L 250 " --> pdb=" O LYS L 246 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N HIS L 251 " --> pdb=" O LEU L 247 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU L 252 " --> pdb=" O LEU L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 270 removed outlier: 4.107A pdb=" N TYR L 259 " --> pdb=" O ASN L 255 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS L 264 " --> pdb=" O THR L 260 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE L 269 " --> pdb=" O GLU L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 273 through 292 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 10 Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 101 Processing sheet with id=AA3, first strand: chain 'A' and resid 135 through 136 removed outlier: 6.610A pdb=" N VAL A 149 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 97 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP A 151 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N MET A 95 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLU A 153 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLY A 93 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ALA A 184 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N MET A 95 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 111 through 113 removed outlier: 5.960A pdb=" N TYR A 112 " --> pdb=" O ILE A 196 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 131 removed outlier: 3.613A pdb=" N GLN A 128 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 279 through 285 removed outlier: 6.125A pdb=" N LEU A 322 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLU A 281 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE A 324 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 283 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 326 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 368 " --> pdb=" O HIS A 323 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET A 372 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE A 256 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N THR A 373 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU A 258 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL A 391 " --> pdb=" O GLY A 255 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 564 through 568 removed outlier: 6.328A pdb=" N PHE A 564 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL A 601 " --> pdb=" O PHE A 564 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS A 566 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 537 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 642 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR A 663 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 540 " --> pdb=" O THR A 663 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 4 through 10 removed outlier: 7.480A pdb=" N VAL B 60 " --> pdb=" O SER B 5 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLN B 7 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE B 62 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA B 9 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N HIS B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 39 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N HIS B 34 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 81 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N SER B 40 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 12.593A pdb=" N GLU B 77 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 135 through 140 removed outlier: 4.412A pdb=" N ILE B 152 " --> pdb=" O ILE B 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 135 through 140 removed outlier: 6.409A pdb=" N THR B 96 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE B 152 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B 94 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N MET B 95 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N GLU B 186 " --> pdb=" O MET B 95 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE B 97 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 112 through 113 removed outlier: 6.476A pdb=" N TYR B 112 " --> pdb=" O ILE B 196 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 128 through 131 Processing sheet with id=AB4, first strand: chain 'B' and resid 283 through 285 removed outlier: 6.452A pdb=" N ILE B 325 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N MET B 372 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N PHE B 327 " --> pdb=" O MET B 372 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 373 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 564 through 568 removed outlier: 6.445A pdb=" N PHE B 564 " --> pdb=" O CYS B 599 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N VAL B 601 " --> pdb=" O PHE B 564 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LYS B 566 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N SER B 598 " --> pdb=" O LEU B 641 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ILE B 643 " --> pdb=" O SER B 598 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL B 600 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N THR B 645 " --> pdb=" O VAL B 600 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL B 602 " --> pdb=" O THR B 645 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL B 539 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N THR B 646 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 541 " --> pdb=" O THR B 646 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 670 through 672 removed outlier: 3.738A pdb=" N ALA B 671 " --> pdb=" O VAL B 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 4 through 10 removed outlier: 6.512A pdb=" N HIS C 43 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N SER C 40 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 12.525A pdb=" N GLU C 77 " --> pdb=" O SER C 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 135 through 139 removed outlier: 4.303A pdb=" N ILE C 152 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN C 170 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 135 through 139 removed outlier: 6.469A pdb=" N THR C 96 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE C 152 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR C 94 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N MET C 95 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N GLU C 186 " --> pdb=" O MET C 95 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE C 97 " --> pdb=" O GLU C 186 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 111 through 113 removed outlier: 6.638A pdb=" N TYR C 112 " --> pdb=" O ILE C 196 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 129 through 131 Processing sheet with id=AC3, first strand: chain 'C' and resid 283 through 284 removed outlier: 3.756A pdb=" N LYS C 283 " --> pdb=" O ILE C 324 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 326 " --> pdb=" O LYS C 283 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N HIS C 323 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N ILE C 370 " --> pdb=" O HIS C 323 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE C 325 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N MET C 372 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET C 393 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR C 259 " --> pdb=" O MET C 393 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 597 through 601 removed outlier: 6.520A pdb=" N SER C 598 " --> pdb=" O LEU C 641 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE C 643 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL C 600 " --> pdb=" O ILE C 643 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N THR C 645 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 642 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 540 " --> pdb=" O THR C 663 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 4 through 10 removed outlier: 7.671A pdb=" N VAL D 60 " --> pdb=" O SER D 5 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLN D 7 " --> pdb=" O VAL D 60 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE D 62 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ALA D 9 " --> pdb=" O PHE D 62 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 135 through 136 removed outlier: 4.373A pdb=" N GLN D 170 " --> pdb=" O ALA D 154 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 135 through 136 removed outlier: 6.684A pdb=" N THR D 96 " --> pdb=" O LYS D 150 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE D 152 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR D 94 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA D 154 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE D 92 " --> pdb=" O ALA D 154 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLY D 93 " --> pdb=" O GLN D 182 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ALA D 184 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N MET D 95 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N GLU D 186 " --> pdb=" O MET D 95 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE D 97 " --> pdb=" O GLU D 186 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 111 through 113 removed outlier: 3.937A pdb=" N ILE D 196 " --> pdb=" O TYR D 112 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 129 through 131 Processing sheet with id=AD1, first strand: chain 'D' and resid 139 through 140 Processing sheet with id=AD2, first strand: chain 'D' and resid 283 through 284 removed outlier: 3.904A pdb=" N LEU D 368 " --> pdb=" O HIS D 323 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR D 373 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 565 through 568 removed outlier: 3.752A pdb=" N LYS D 566 " --> pdb=" O CYS D 599 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL D 601 " --> pdb=" O LYS D 566 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS D 568 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER D 598 " --> pdb=" O LEU D 641 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ILE D 643 " --> pdb=" O SER D 598 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL D 600 " --> pdb=" O ILE D 643 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N THR D 645 " --> pdb=" O VAL D 600 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL D 602 " --> pdb=" O THR D 645 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 258 through 259 Processing sheet with id=AD5, first strand: chain 'E' and resid 283 through 285 removed outlier: 6.179A pdb=" N LYS E 283 " --> pdb=" O ILE E 326 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASP E 328 " --> pdb=" O LYS E 283 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL E 285 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET E 372 " --> pdb=" O PHE E 327 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 540 through 542 removed outlier: 3.677A pdb=" N THR E 646 " --> pdb=" O LEU E 541 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS E 566 " --> pdb=" O CYS E 599 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 258 through 259 removed outlier: 7.053A pdb=" N LEU F 258 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE F 325 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE F 370 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N MET F 372 " --> pdb=" O PHE F 327 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASN F 286 " --> pdb=" O ASP F 328 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 564 through 568 removed outlier: 4.325A pdb=" N CYS F 599 " --> pdb=" O PHE F 564 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS F 566 " --> pdb=" O CYS F 599 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU F 641 " --> pdb=" O SER F 598 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL F 537 " --> pdb=" O ILE F 642 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N GLY F 644 " --> pdb=" O VAL F 537 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL F 539 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N THR F 646 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU F 541 " --> pdb=" O THR F 646 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR F 663 " --> pdb=" O SER F 538 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LEU F 540 " --> pdb=" O THR F 663 " (cutoff:3.500A) 1622 hydrogen bonds defined for protein. 4737 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: 27.88 Time building geometry restraints manager: 17.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.02: 36542 1.02 - 1.22: 83 1.22 - 1.42: 14796 1.42 - 1.62: 21946 1.62 - 1.83: 358 Bond restraints: 73725 Sorted by residual: bond pdb=" C4 ATP B 802 " pdb=" N9 ATP B 802 " ideal model delta sigma weight residual 1.374 1.296 0.078 1.00e-02 1.00e+04 6.14e+01 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.41e+01 bond pdb=" C5 ATP D 802 " pdb=" N7 ATP D 802 " ideal model delta sigma weight residual 1.387 1.315 0.072 1.00e-02 1.00e+04 5.24e+01 bond pdb=" C4 ATP D 801 " pdb=" C5 ATP D 801 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.73e+01 bond pdb=" C4 ATP D 802 " pdb=" C5 ATP D 802 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.71e+01 ... (remaining 73720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.87: 133248 5.87 - 11.74: 417 11.74 - 17.61: 20 17.61 - 23.48: 10 23.48 - 29.35: 15 Bond angle restraints: 133710 Sorted by residual: angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 107.48 29.35 1.00e+00 1.00e+00 8.61e+02 angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 111.56 28.31 1.00e+00 1.00e+00 8.02e+02 angle pdb=" PB ATP D 802 " pdb=" O3B ATP D 802 " pdb=" PG ATP D 802 " ideal model delta sigma weight residual 139.87 112.29 27.58 1.00e+00 1.00e+00 7.61e+02 angle pdb=" PB ATP E 801 " pdb=" O3B ATP E 801 " pdb=" PG ATP E 801 " ideal model delta sigma weight residual 139.87 113.97 25.90 1.00e+00 1.00e+00 6.71e+02 angle pdb=" PB ATP F 801 " pdb=" O3B ATP F 801 " pdb=" PG ATP F 801 " ideal model delta sigma weight residual 139.87 114.03 25.84 1.00e+00 1.00e+00 6.68e+02 ... (remaining 133705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 33723 35.96 - 71.92: 602 71.92 - 107.89: 28 107.89 - 143.85: 4 143.85 - 179.81: 3 Dihedral angle restraints: 34360 sinusoidal: 19402 harmonic: 14958 Sorted by residual: dihedral pdb=" CD ARG A 388 " pdb=" NE ARG A 388 " pdb=" CZ ARG A 388 " pdb=" NH1 ARG A 388 " ideal model delta sinusoidal sigma weight residual 0.00 -179.81 179.81 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA LEU K 75 " pdb=" C LEU K 75 " pdb=" N GLN K 76 " pdb=" CA GLN K 76 " ideal model delta harmonic sigma weight residual 180.00 142.83 37.17 0 5.00e+00 4.00e-02 5.53e+01 dihedral pdb=" CA PHE L 206 " pdb=" C PHE L 206 " pdb=" N PHE L 207 " pdb=" CA PHE L 207 " ideal model delta harmonic sigma weight residual 180.00 143.18 36.82 0 5.00e+00 4.00e-02 5.42e+01 ... (remaining 34357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.560: 5668 0.560 - 1.121: 0 1.121 - 1.681: 2 1.681 - 2.241: 1 2.241 - 2.801: 1 Chirality restraints: 5672 Sorted by residual: chirality pdb=" CG LEU C 484 " pdb=" CB LEU C 484 " pdb=" CD1 LEU C 484 " pdb=" CD2 LEU C 484 " both_signs ideal model delta sigma weight residual False -2.59 0.21 -2.80 2.00e-01 2.50e+01 1.96e+02 chirality pdb=" CB VAL F 698 " pdb=" CA VAL F 698 " pdb=" CG1 VAL F 698 " pdb=" CG2 VAL F 698 " both_signs ideal model delta sigma weight residual False -2.63 -0.91 -1.72 2.00e-01 2.50e+01 7.42e+01 chirality pdb=" CB VAL B 346 " pdb=" CA VAL B 346 " pdb=" CG1 VAL B 346 " pdb=" CG2 VAL B 346 " both_signs ideal model delta sigma weight residual False -2.63 -1.03 -1.60 2.00e-01 2.50e+01 6.38e+01 ... (remaining 5669 not shown) Planarity restraints: 10896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 495 " 0.060 2.00e-02 2.50e+03 7.80e-02 9.14e+01 pdb=" CG ASN B 495 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN B 495 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 495 " -0.125 2.00e-02 2.50e+03 pdb="HD21 ASN B 495 " -0.012 2.00e-02 2.50e+03 pdb="HD22 ASN B 495 " 0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 495 " -0.060 2.00e-02 2.50e+03 7.55e-02 8.55e+01 pdb=" CG ASN D 495 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN D 495 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN D 495 " 0.118 2.00e-02 2.50e+03 pdb="HD21 ASN D 495 " 0.008 2.00e-02 2.50e+03 pdb="HD22 ASN D 495 " -0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 405 " -0.031 2.00e-02 2.50e+03 6.76e-02 6.85e+01 pdb=" CD GLN B 405 " 0.140 2.00e-02 2.50e+03 pdb=" OE1 GLN B 405 " -0.062 2.00e-02 2.50e+03 pdb=" NE2 GLN B 405 " -0.051 2.00e-02 2.50e+03 pdb="HE21 GLN B 405 " -0.011 2.00e-02 2.50e+03 pdb="HE22 GLN B 405 " 0.015 2.00e-02 2.50e+03 ... (remaining 10893 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 4023 2.18 - 2.79: 155858 2.79 - 3.39: 195398 3.39 - 4.00: 253400 4.00 - 4.60: 392942 Nonbonded interactions: 1001621 Sorted by model distance: nonbonded pdb="HH22 ARG E 607 " pdb=" O TYR E 611 " model vdw 1.579 2.450 nonbonded pdb=" O ASP L 267 " pdb="HH11 ARG L 271 " model vdw 1.579 2.450 nonbonded pdb=" OD1 ASP A 229 " pdb="HH21 ARG A 233 " model vdw 1.589 2.450 nonbonded pdb=" HZ2 LYS F 708 " pdb=" O3A ATP F 801 " model vdw 1.591 2.450 nonbonded pdb=" O ASN L 220 " pdb=" H ALA L 224 " model vdw 1.607 2.450 ... (remaining 1001616 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB or name OG or name HA or name HB2 or name HB3)) or resid 7 \ 4 through 87 or (resid 88 and (name N or name CA or name C or name O or name CB \ or name HA or name HB1 or name HB2 or name HB3)) or resid 89 through 199 or (res \ id 200 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 or name HG \ 2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or nam \ e HZ3)) or resid 201 through 215 or (resid 216 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA or \ name HB2 or name HB3 or name HG2 or name HG3)) or resid 217 through 457 or resi \ d 459 through 547 or (resid 548 and (name N or name CA or name C or name O or na \ me HA2 or name HA3)) or resid 549 through 738 or resid 801)) selection = (chain 'B' and (resid 1 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB or name OG or name HA or name HB2 or name HB3)) or resid 7 \ 4 through 87 or (resid 88 and (name N or name CA or name C or name O or name CB \ or name HA or name HB1 or name HB2 or name HB3)) or resid 89 through 201 or resi \ d 211 through 215 or (resid 216 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or na \ me HB3 or name HG2 or name HG3)) or resid 217 through 263 or (resid 264 and (nam \ e N or name CA or name C or name O or name CB or name SG or name HA or name HB2 \ or name HB3 or name HG )) or resid 265 through 387 or (resid 388 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or name \ HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or \ name HH21)) or resid 389 through 457 or resid 459 or (resid 477 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name NE or name C \ Z or name NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name \ HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 o \ r name HH22)) or resid 478 through 547 or (resid 548 and (name N or name CA or n \ ame C or name O or name HA2 or name HA3)) or resid 549 through 738 or resid 801) \ ) selection = (chain 'C' and (resid 1 through 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name H or \ name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 \ or name HE2 or name HE3 or name HZ1 or name HZ3)) or (resid 201 and (name N or \ name CA or name C or name O or name CB or name OG1 or name CG2 or name HA or nam \ e HB or name HG21 or name HG22 or name HG23)) or resid 211 through 263 or (resid \ 264 and (name N or name CA or name C or name O or name CB or name SG or name HA \ or name HB2 or name HB3 or name HG )) or resid 265 through 387 or (resid 388 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD or nam \ e NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name \ HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or \ name HH12 or name HH21)) or resid 389 through 457 or resid 470 or (resid 477 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ NE or name CZ or name NH1 or name NH2 or name HA or name HB2 or name HB3 or nam \ e HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 o \ r name HH21 or name HH22)) or resid 478 through 547 or (resid 548 and (name N or \ name CA or name C or name O or name HA2 or name HA3)) or resid 549 through 738 \ or resid 801)) selection = (chain 'D' and (resid 1 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB or name OG or name HA or name HB2 or name HB3)) or resid 7 \ 4 through 87 or (resid 88 and (name N or name CA or name C or name O or name CB \ or name HA or name HB1 or name HB2 or name HB3)) or resid 89 through 199 or (res \ id 200 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 or name HG \ 2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or nam \ e HZ3)) or (resid 201 and (name N or name CA or name C or name O or name CB or n \ ame OG1 or name CG2 or name HA or name HB or name HG21 or name HG22 or name HG23 \ )) or resid 211 through 215 or (resid 216 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD or name OE1 or name OE2 or name HA or name \ HB2 or name HB3 or name HG2 or name HG3)) or resid 217 through 263 or (resid 26 \ 4 and (name N or name CA or name C or name O or name CB or name SG or name HA or \ name HB2 or name HB3 or name HG )) or resid 265 through 387 or (resid 388 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD or name N \ E or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB \ 3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or nam \ e HH12 or name HH21)) or resid 389 through 457 or resid 470 or (resid 477 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name CZ or name NH1 or name NH2 or name HA or name HB2 or name HB3 or name H \ G2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or n \ ame HH21 or name HH22)) or resid 478 through 738 or resid 801)) } ncs_group { reference = (chain 'E' and (resid 219 through 222 or (resid 223 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 224 through 237 or (r \ esid 238 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 239 or (resid 251 through 252 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 253 or (resid 254 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 25 \ 5 through 265 or (resid 266 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 267 through 268 or (resid 269 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 270 thro \ ugh 274 or (resid 275 through 278 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 279 or (resid 280 through 281 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 28 \ 2 or (resid 283 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 284 through 288 or (resid 289 through 295 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 296 or ( \ resid 297 through 298 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 299 through 301 or (resid 302 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 303 through 32 \ 4 or (resid 325 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 326 through 328 or (resid 329 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 330 or (resid 347 an \ d (name N or name CA or name C or name O or name CB or name HA )) or (resid 348 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 349 through 351 or (resid 352 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 353 through 358 or (resid 359 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 360 or (resid 361 through 364 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 365 or (resid 366 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 367 through 382 o \ r (resid 383 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 384 through 389 or (resid 390 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 398 through 414 or resi \ d 422 through 457 or (resid 471 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or na \ me HB3 or name HG2 or name HG3)) or resid 472 through 738 or resid 801)) selection = chain 'F' } ncs_group { reference = chain 'K' selection = (chain 'L' and (resid 8 through 49 or (resid 50 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or \ name HB2 or name HB3 or name HD22)) or resid 51 through 221 or (resid 222 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 223 through 292 or (resid 293 and (name N or name CA or name C or name O or na \ me CB or name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)))) } 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 group one per residue 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: 0.750 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: 0.970 Extract box with map and model: 2.080 Check model and map are aligned: 0.420 Set scattering table: 0.520 Process input model: 119.720 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.220 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:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 0.013 0.130 37121 Z= 0.821 Angle : 1.546 29.349 50060 Z= 0.936 Chirality : 0.094 2.801 5672 Planarity : 0.009 0.128 6447 Dihedral : 12.232 179.810 14343 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.90 % Favored : 95.82 % Rotamer: Outliers : 0.10 % Allowed : 5.31 % Favored : 94.59 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.62 (0.10), residues: 4589 helix: -2.56 (0.09), residues: 1967 sheet: -2.31 (0.17), residues: 593 loop : -2.08 (0.12), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP F 704 HIS 0.037 0.005 HIS A 323 PHE 0.071 0.006 PHE L 235 TYR 0.060 0.006 TYR K 152 ARG 0.029 0.002 ARG D 238 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 280 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 276 time to evaluate : 4.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 ASN cc_start: 0.9152 (t160) cc_final: 0.8889 (p0) REVERT: C 276 MET cc_start: 0.8096 (mpt) cc_final: 0.7727 (tmm) REVERT: H 202 MET cc_start: 0.7987 (mtm) cc_final: 0.7440 (ttp) REVERT: I 215 MET cc_start: 0.8613 (mtm) cc_final: 0.7787 (mtp) outliers start: 4 outliers final: 3 residues processed: 280 average time/residue: 1.0265 time to fit residues: 445.4132 Evaluate side-chains 222 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 219 time to evaluate : 4.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 387 optimal weight: 6.9990 chunk 347 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 234 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 359 optimal weight: 2.9990 chunk 139 optimal weight: 30.0000 chunk 218 optimal weight: 7.9990 chunk 267 optimal weight: 1.9990 chunk 416 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN B 435 ASN B 505 ASN ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 ASN B 696 GLN ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 141 ASN C 190 ASN C 374 ASN ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN D 435 ASN D 449 GLN D 530 ASN D 659 ASN E 214 ASN E 696 GLN E 719 GLN F 286 ASN F 313 GLN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 ASN ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 254 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 37121 Z= 0.237 Angle : 0.736 12.438 50060 Z= 0.400 Chirality : 0.061 1.858 5672 Planarity : 0.005 0.058 6447 Dihedral : 11.104 178.633 5264 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.11), residues: 4589 helix: -1.80 (0.10), residues: 2057 sheet: -1.89 (0.18), residues: 593 loop : -1.91 (0.13), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 704 HIS 0.009 0.001 HIS A 323 PHE 0.024 0.002 PHE E 327 TYR 0.020 0.002 TYR L 266 ARG 0.013 0.001 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 4.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.7555 (tpp) cc_final: 0.7344 (tpp) REVERT: A 453 MET cc_start: 0.8315 (tpt) cc_final: 0.7572 (tpt) REVERT: H 202 MET cc_start: 0.7811 (mtm) cc_final: 0.6589 (tmm) REVERT: K 215 CYS cc_start: 0.8171 (t) cc_final: 0.7923 (t) REVERT: L 51 MET cc_start: 0.7715 (ppp) cc_final: 0.7408 (ppp) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 1.0839 time to fit residues: 434.7240 Evaluate side-chains 231 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 4.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 231 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 346 optimal weight: 10.0000 chunk 283 optimal weight: 20.0000 chunk 114 optimal weight: 8.9990 chunk 417 optimal weight: 20.0000 chunk 451 optimal weight: 10.0000 chunk 371 optimal weight: 10.0000 chunk 414 optimal weight: 6.9990 chunk 142 optimal weight: 20.0000 chunk 334 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 ASN A 669 ASN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 ASN ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 GLN D 374 ASN D 659 ASN E 301 ASN ** E 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 57 ASN ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 37121 Z= 0.267 Angle : 0.671 10.982 50060 Z= 0.368 Chirality : 0.058 1.782 5672 Planarity : 0.004 0.052 6447 Dihedral : 10.583 175.146 5264 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.40 % Favored : 94.57 % Rotamer: Outliers : 0.08 % Allowed : 1.86 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.11), residues: 4589 helix: -1.32 (0.10), residues: 2085 sheet: -1.71 (0.18), residues: 628 loop : -1.78 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 213 HIS 0.007 0.001 HIS K 251 PHE 0.021 0.002 PHE E 327 TYR 0.019 0.002 TYR F 724 ARG 0.015 0.001 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 247 time to evaluate : 4.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 MET cc_start: 0.8416 (tpt) cc_final: 0.7697 (tpt) REVERT: K 51 MET cc_start: 0.8696 (ppp) cc_final: 0.8275 (ppp) outliers start: 3 outliers final: 0 residues processed: 250 average time/residue: 1.1292 time to fit residues: 441.5076 Evaluate side-chains 223 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 4.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 412 optimal weight: 9.9990 chunk 313 optimal weight: 5.9990 chunk 216 optimal weight: 50.0000 chunk 46 optimal weight: 0.3980 chunk 199 optimal weight: 8.9990 chunk 280 optimal weight: 20.0000 chunk 419 optimal weight: 9.9990 chunk 443 optimal weight: 20.0000 chunk 218 optimal weight: 50.0000 chunk 397 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 overall best weight: 7.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 ASN ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 ASN D 301 ASN D 418 GLN ** E 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 ASN ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 37121 Z= 0.258 Angle : 0.634 10.892 50060 Z= 0.349 Chirality : 0.057 1.754 5672 Planarity : 0.004 0.043 6447 Dihedral : 10.468 176.658 5264 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.03 % Allowed : 1.58 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.11), residues: 4589 helix: -1.08 (0.10), residues: 2100 sheet: -1.63 (0.19), residues: 614 loop : -1.75 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 213 HIS 0.008 0.001 HIS K 251 PHE 0.020 0.002 PHE E 327 TYR 0.018 0.002 TYR C 611 ARG 0.011 0.001 ARG B 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 4.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 MET cc_start: 0.6442 (mtp) cc_final: 0.6155 (mtp) REVERT: A 453 MET cc_start: 0.8615 (tpt) cc_final: 0.7914 (tpt) REVERT: C 218 MET cc_start: 0.7494 (mpp) cc_final: 0.7090 (mpp) REVERT: F 504 MET cc_start: 0.8146 (ptm) cc_final: 0.7503 (tmm) REVERT: F 573 MET cc_start: 0.7854 (pmm) cc_final: 0.7647 (pmm) REVERT: K 51 MET cc_start: 0.8735 (ppp) cc_final: 0.8240 (ppp) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 1.0741 time to fit residues: 397.5929 Evaluate side-chains 214 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 4.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 369 optimal weight: 10.0000 chunk 251 optimal weight: 9.9990 chunk 6 optimal weight: 30.0000 chunk 330 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 378 optimal weight: 20.0000 chunk 306 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 226 optimal weight: 40.0000 chunk 398 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN B 659 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 GLN E 374 ASN E 435 ASN H 159 ASN ** L 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 37121 Z= 0.315 Angle : 0.668 10.793 50060 Z= 0.369 Chirality : 0.057 1.746 5672 Planarity : 0.005 0.046 6447 Dihedral : 10.467 175.559 5264 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.11), residues: 4589 helix: -1.11 (0.10), residues: 2114 sheet: -1.73 (0.19), residues: 638 loop : -1.79 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 704 HIS 0.009 0.002 HIS K 251 PHE 0.023 0.002 PHE E 327 TYR 0.021 0.002 TYR D 611 ARG 0.006 0.001 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 4.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 MET cc_start: 0.8627 (tpt) cc_final: 0.8024 (tpt) REVERT: C 218 MET cc_start: 0.7822 (mpp) cc_final: 0.7515 (mpp) REVERT: F 453 MET cc_start: 0.7102 (ttt) cc_final: 0.6751 (ttp) REVERT: F 504 MET cc_start: 0.8218 (ptm) cc_final: 0.7735 (tmm) REVERT: H 167 MET cc_start: 0.9177 (ptp) cc_final: 0.8817 (ptp) REVERT: K 51 MET cc_start: 0.8774 (ppp) cc_final: 0.8530 (ppp) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 1.0499 time to fit residues: 377.1768 Evaluate side-chains 216 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 4.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 149 optimal weight: 10.0000 chunk 399 optimal weight: 9.9990 chunk 87 optimal weight: 30.0000 chunk 260 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 444 optimal weight: 20.0000 chunk 368 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 233 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN B 301 ASN B 659 ASN ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 GLN D 659 ASN E 374 ASN ** L 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 37121 Z= 0.236 Angle : 0.608 10.897 50060 Z= 0.331 Chirality : 0.057 1.765 5672 Planarity : 0.004 0.045 6447 Dihedral : 10.269 175.311 5264 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.03 % Allowed : 1.58 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.11), residues: 4589 helix: -0.90 (0.10), residues: 2135 sheet: -1.72 (0.19), residues: 622 loop : -1.72 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 213 HIS 0.007 0.001 HIS K 251 PHE 0.020 0.002 PHE E 327 TYR 0.020 0.002 TYR F 593 ARG 0.005 0.000 ARG D 691 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 4.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 MET cc_start: 0.8607 (tpt) cc_final: 0.8032 (tpt) REVERT: C 655 MET cc_start: 0.7942 (ptp) cc_final: 0.7469 (ptp) REVERT: F 453 MET cc_start: 0.7081 (ttt) cc_final: 0.6713 (ttp) REVERT: F 504 MET cc_start: 0.8151 (ptm) cc_final: 0.7682 (tmm) REVERT: K 51 MET cc_start: 0.8796 (ppp) cc_final: 0.8539 (ppp) outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 1.0165 time to fit residues: 355.1628 Evaluate side-chains 210 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 4.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 428 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 253 optimal weight: 5.9990 chunk 324 optimal weight: 20.0000 chunk 251 optimal weight: 9.9990 chunk 373 optimal weight: 2.9990 chunk 247 optimal weight: 10.0000 chunk 442 optimal weight: 10.0000 chunk 276 optimal weight: 5.9990 chunk 269 optimal weight: 8.9990 chunk 204 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN B 301 ASN B 659 ASN ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 GLN D 418 GLN ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 ASN E 685 ASN ** L 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 37121 Z= 0.230 Angle : 0.599 10.802 50060 Z= 0.325 Chirality : 0.057 1.746 5672 Planarity : 0.004 0.052 6447 Dihedral : 10.156 175.124 5264 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.03 % Allowed : 1.30 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.12), residues: 4589 helix: -0.78 (0.10), residues: 2132 sheet: -1.79 (0.19), residues: 609 loop : -1.68 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 510 HIS 0.007 0.001 HIS K 251 PHE 0.018 0.002 PHE E 327 TYR 0.017 0.002 TYR D 611 ARG 0.008 0.000 ARG C 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 4.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 MET cc_start: 0.8611 (tpt) cc_final: 0.8078 (tpt) REVERT: C 218 MET cc_start: 0.7832 (mpp) cc_final: 0.7470 (mpp) REVERT: C 655 MET cc_start: 0.7850 (ptp) cc_final: 0.7204 (ptp) REVERT: F 504 MET cc_start: 0.8117 (ptm) cc_final: 0.7742 (tmm) REVERT: H 1 MET cc_start: 0.2445 (ttm) cc_final: 0.2101 (tpp) REVERT: K 51 MET cc_start: 0.8810 (ppp) cc_final: 0.8564 (ppp) outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 1.0046 time to fit residues: 355.4487 Evaluate side-chains 207 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 4.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 273 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 264 optimal weight: 0.8980 chunk 133 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 281 optimal weight: 20.0000 chunk 301 optimal weight: 6.9990 chunk 218 optimal weight: 30.0000 chunk 41 optimal weight: 5.9990 chunk 347 optimal weight: 0.3980 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN B 301 ASN B 374 ASN B 659 ASN ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 ASN ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37121 Z= 0.172 Angle : 0.575 10.825 50060 Z= 0.305 Chirality : 0.057 1.746 5672 Planarity : 0.004 0.058 6447 Dihedral : 9.954 178.245 5264 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.03 % Allowed : 0.61 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.12), residues: 4589 helix: -0.47 (0.11), residues: 2152 sheet: -1.67 (0.19), residues: 606 loop : -1.52 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 510 HIS 0.005 0.001 HIS K 251 PHE 0.020 0.001 PHE F 589 TYR 0.013 0.001 TYR D 611 ARG 0.007 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 224 time to evaluate : 4.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 MET cc_start: 0.8581 (tpt) cc_final: 0.8033 (tpt) REVERT: F 453 MET cc_start: 0.7078 (ttt) cc_final: 0.6630 (ttp) REVERT: F 504 MET cc_start: 0.8007 (ptm) cc_final: 0.7438 (tmm) REVERT: K 51 MET cc_start: 0.8806 (ppp) cc_final: 0.8548 (ppp) outliers start: 1 outliers final: 1 residues processed: 225 average time/residue: 1.0150 time to fit residues: 363.5820 Evaluate side-chains 214 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 4.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 402 optimal weight: 20.0000 chunk 423 optimal weight: 9.9990 chunk 386 optimal weight: 9.9990 chunk 412 optimal weight: 3.9990 chunk 248 optimal weight: 8.9990 chunk 179 optimal weight: 9.9990 chunk 323 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 372 optimal weight: 0.7980 chunk 389 optimal weight: 9.9990 chunk 410 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 ASN ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN B 301 ASN ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 GLN D 675 GLN ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37121 Z= 0.211 Angle : 0.579 11.125 50060 Z= 0.313 Chirality : 0.056 1.734 5672 Planarity : 0.004 0.041 6447 Dihedral : 9.845 178.622 5264 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.03 % Allowed : 0.56 % Favored : 99.41 % 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: -1.67 (0.12), residues: 4589 helix: -0.45 (0.11), residues: 2141 sheet: -1.68 (0.19), residues: 625 loop : -1.53 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 510 HIS 0.006 0.001 HIS K 251 PHE 0.016 0.002 PHE F 231 TYR 0.017 0.002 TYR D 611 ARG 0.005 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 4.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 MET cc_start: 0.8641 (tpt) cc_final: 0.8119 (tpt) REVERT: F 453 MET cc_start: 0.7093 (ttt) cc_final: 0.6688 (ttp) REVERT: F 504 MET cc_start: 0.8078 (ptm) cc_final: 0.7508 (tmm) REVERT: K 51 MET cc_start: 0.8806 (ppp) cc_final: 0.8507 (ppp) outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 0.9956 time to fit residues: 348.2651 Evaluate side-chains 208 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 4.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 270 optimal weight: 6.9990 chunk 435 optimal weight: 9.9990 chunk 266 optimal weight: 10.0000 chunk 206 optimal weight: 3.9990 chunk 303 optimal weight: 10.0000 chunk 457 optimal weight: 20.0000 chunk 420 optimal weight: 6.9990 chunk 364 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 281 optimal weight: 10.0000 chunk 223 optimal weight: 50.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN B 301 ASN ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 ASN ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 37121 Z= 0.227 Angle : 0.590 10.658 50060 Z= 0.319 Chirality : 0.056 1.736 5672 Planarity : 0.004 0.039 6447 Dihedral : 9.783 178.094 5264 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.03 % Allowed : 0.28 % Favored : 99.69 % 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: -1.69 (0.12), residues: 4589 helix: -0.46 (0.11), residues: 2130 sheet: -1.77 (0.19), residues: 617 loop : -1.53 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 704 HIS 0.006 0.001 HIS K 251 PHE 0.020 0.002 PHE B 327 TYR 0.016 0.002 TYR D 611 ARG 0.005 0.001 ARG J 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9178 Ramachandran restraints generated. 4589 Oldfield, 0 Emsley, 4589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 201 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue THR 201 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 266 is missing expected H atoms. Skipping. Residue LEU 269 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue LEU 277 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 290 is missing expected H atoms. Skipping. Residue LEU 291 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue VAL 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue ILE 325 is missing expected H atoms. Skipping. Residue VAL 361 is missing expected H atoms. Skipping. Residue LEU 364 is missing expected H atoms. Skipping. Residue LEU 383 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 4.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 MET cc_start: 0.8667 (tpt) cc_final: 0.8217 (tpt) REVERT: E 589 PHE cc_start: 0.8245 (m-80) cc_final: 0.8002 (m-10) REVERT: F 453 MET cc_start: 0.7128 (ttt) cc_final: 0.6719 (ttp) REVERT: F 504 MET cc_start: 0.8110 (ptm) cc_final: 0.7619 (tmm) REVERT: H 202 MET cc_start: 0.7929 (mtp) cc_final: 0.7210 (tmm) outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 1.0507 time to fit residues: 374.6590 Evaluate side-chains 211 residues out of total 3960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 4.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 289 optimal weight: 20.0000 chunk 387 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 335 optimal weight: 50.0000 chunk 53 optimal weight: 8.9990 chunk 101 optimal weight: 20.0000 chunk 364 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 374 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 overall best weight: 7.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 ASN ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 ASN F 454 ASN ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.039310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.028176 restraints weight = 1819376.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.029166 restraints weight = 706455.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.029740 restraints weight = 356551.799| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 37121 Z= 0.286 Angle : 0.634 10.235 50060 Z= 0.347 Chirality : 0.056 1.742 5672 Planarity : 0.004 0.041 6447 Dihedral : 9.806 178.117 5264 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.03 % Allowed : 0.38 % Favored : 99.59 % 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: -1.92 (0.12), residues: 4589 helix: -0.65 (0.11), residues: 2133 sheet: -1.88 (0.19), residues: 639 loop : -1.62 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 704 HIS 0.008 0.002 HIS B 456 PHE 0.021 0.002 PHE C 576 TYR 0.019 0.002 TYR L 266 ARG 0.006 0.001 ARG J 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9906.85 seconds wall clock time: 172 minutes 6.23 seconds (10326.23 seconds total)