Starting phenix.real_space_refine on Sun Sep 29 08:33:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdn_9101/09_2024/6mdn_9101_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdn_9101/09_2024/6mdn_9101.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/6mdn_9101/09_2024/6mdn_9101.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdn_9101/09_2024/6mdn_9101.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdn_9101/09_2024/6mdn_9101_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdn_9101/09_2024/6mdn_9101_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 22882 2.51 5 N 6311 2.21 5 O 6980 1.98 5 H 36496 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 44 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: 72910 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 8082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 8082 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 22, 'TRANS': 488} Chain breaks: 1 Chain: "B" Number of atoms: 11129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 11129 Classifications: {'peptide': 707} Link IDs: {'PTRANS': 29, 'TRANS': 677} Chain breaks: 3 Chain: "C" Number of atoms: 11167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 709, 11167 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: 10987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 10987 Classifications: {'peptide': 697} Link IDs: {'PTRANS': 26, 'TRANS': 670} Chain breaks: 4 Chain: "F" Number of atoms: 6748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 6748 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 18, 'TRANS': 430} Chain breaks: 5 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "H" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2295 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: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1063 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: 4436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4436 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: 4454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4454 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: 25.62, per 1000 atoms: 0.35 Number of scatterers: 72910 At special positions: 0 Unit cell: (154.58, 146.72, 227.94, 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 6980 8.00 N 6311 7.00 C 22882 6.00 H 36496 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 Atom "HETATM72691 O3B ATP B 802 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.53 Conformation dependent library (CDL) restraints added in 4.6 seconds 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8652 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 34 sheets defined 52.4% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.52 Creating SS restraints... Processing helix chain 'A' and resid 223 through 234 removed outlier: 3.504A pdb=" N PHE A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 249 removed outlier: 4.199A pdb=" N VAL A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN A 247 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.739A pdb=" N ARG A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 317 removed outlier: 4.274A pdb=" N SER A 298 " --> pdb=" O TYR A 294 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLU A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 349 through 359 removed outlier: 4.114A pdb=" N GLN A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 418 removed outlier: 4.395A pdb=" N ARG A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N MET A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 432 removed outlier: 3.805A pdb=" N VAL A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 456 removed outlier: 3.512A pdb=" N GLU A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 3.660A 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: 3.981A pdb=" N TYR A 502 " --> pdb=" O ASP A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 530 removed outlier: 3.638A pdb=" N THR A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 560 removed outlier: 4.256A 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 579 through 594 removed outlier: 3.635A pdb=" N GLN A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 619 through 631 removed outlier: 3.967A pdb=" N LEU A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) removed outlier: 3.862A 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: 3.949A pdb=" N GLU A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 698 removed outlier: 3.788A pdb=" N ILE A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 719 removed outlier: 3.674A pdb=" N GLN A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 734 removed outlier: 4.539A pdb=" N VAL A 726 " --> pdb=" O PRO A 722 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ARG A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.676A pdb=" N LEU B 18 " --> pdb=" O GLU B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 114 through 125 Processing helix chain 'B' and resid 223 through 240 removed outlier: 3.505A pdb=" N ALA B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N SER B 237 " --> pdb=" O ARG B 233 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 249 removed outlier: 3.603A 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: 4.216A pdb=" N ILE B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU B 305 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 removed outlier: 4.238A pdb=" N ILE B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 359 removed outlier: 3.691A pdb=" N ASP B 359 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.838A pdb=" N LEU B 378 " --> pdb=" O ARG B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 Processing helix chain 'B' and resid 399 through 417 removed outlier: 3.859A pdb=" N LEU B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG B 413 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N MET B 414 " --> pdb=" O HIS B 410 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N HIS B 417 " --> pdb=" O ARG B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 433 Processing helix chain 'B' and resid 437 through 455 removed outlier: 3.972A pdb=" N GLU B 442 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 486 Processing helix chain 'B' and resid 498 through 502 removed outlier: 3.768A pdb=" N SER B 501 " --> pdb=" O ASP B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 530 removed outlier: 4.142A pdb=" N THR B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 560 Processing helix chain 'B' and resid 569 through 573 Processing helix chain 'B' and resid 577 through 593 removed outlier: 3.552A 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 Processing helix chain 'B' and resid 687 through 698 Processing helix chain 'B' and resid 706 through 719 removed outlier: 3.932A pdb=" N MET B 712 " --> pdb=" O LYS B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 735 removed outlier: 4.204A pdb=" N VAL B 726 " --> pdb=" O PRO B 722 " (cutoff:3.500A) removed outlier: 4.629A 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 68 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 114 through 125 removed outlier: 3.549A pdb=" N ALA C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 236 removed outlier: 3.506A pdb=" N SER C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 249 Processing helix chain 'C' and resid 265 through 277 Processing helix chain 'C' and resid 296 through 307 removed outlier: 3.852A pdb=" N ILE C 302 " --> pdb=" O SER C 298 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG C 303 " --> pdb=" O GLU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 317 Processing helix chain 'C' and resid 347 through 359 removed outlier: 3.897A pdb=" N VAL C 351 " --> pdb=" O HIS C 347 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 356 " --> pdb=" O ASN C 352 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP C 359 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 removed outlier: 3.504A pdb=" N LEU C 378 " --> pdb=" O ARG C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 Processing helix chain 'C' and resid 399 through 417 removed outlier: 3.545A pdb=" N LEU C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N MET C 414 " --> pdb=" O HIS C 410 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS C 417 " --> pdb=" O ARG C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 433 removed outlier: 3.953A pdb=" N LEU C 429 " --> pdb=" O ASP C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 457 Processing helix chain 'C' and resid 480 through 486 Processing helix chain 'C' and resid 496 through 503 removed outlier: 4.511A pdb=" N ALA C 500 " --> pdb=" O GLN C 496 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 501 " --> pdb=" O GLU C 497 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR C 502 " --> pdb=" O ASP C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 531 removed outlier: 3.569A pdb=" N THR C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 561 removed outlier: 3.635A 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: 3.675A 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 687 through 699 removed outlier: 4.061A pdb=" N THR C 693 " --> pdb=" O LYS C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 719 removed outlier: 4.084A pdb=" N MET C 712 " --> pdb=" O LYS C 708 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU C 715 " --> pdb=" O LEU C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 738 removed outlier: 4.558A pdb=" N VAL C 726 " --> pdb=" O PRO C 722 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ARG C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU C 735 " --> pdb=" O ALA C 731 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU C 736 " --> pdb=" O LEU C 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 19 Processing helix chain 'D' and resid 63 through 71 Processing helix chain 'D' and resid 114 through 125 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: 3.678A pdb=" N LEU D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLY D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 291 removed outlier: 4.291A pdb=" N ILE D 290 " --> pdb=" O GLY D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 316 removed outlier: 4.093A pdb=" N LYS D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU D 305 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE D 306 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ASP D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 348 removed outlier: 3.975A 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: 4.338A pdb=" N GLN D 353 " --> pdb=" O THR D 349 " (cutoff:3.500A) removed outlier: 3.585A 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 399 through 417 removed outlier: 3.506A pdb=" N LEU D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS D 410 " --> pdb=" O ILE D 406 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ARG D 413 " --> pdb=" O ILE D 409 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N MET D 414 " --> pdb=" O HIS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 432 removed outlier: 3.597A pdb=" N GLU D 432 " --> pdb=" O GLU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 458 removed outlier: 4.190A pdb=" N LEU D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG D 455 " --> pdb=" O THR D 451 " (cutoff:3.500A) removed outlier: 4.223A 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: 3.881A pdb=" N THR D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN D 526 " --> pdb=" O GLU D 522 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN D 527 " --> pdb=" O LEU D 523 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR D 528 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 removed outlier: 3.705A pdb=" N ALA D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 594 removed outlier: 4.023A pdb=" N MET D 585 " --> pdb=" O LYS D 581 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 609 Processing helix chain 'D' and resid 619 through 631 removed outlier: 4.030A pdb=" N LEU D 623 " --> pdb=" O SER D 619 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS D 631 " --> pdb=" O LEU D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 638 removed outlier: 4.246A pdb=" N GLY D 637 " --> pdb=" O PRO D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 656 removed outlier: 3.668A pdb=" N MET D 655 " --> pdb=" O VAL D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 661 removed outlier: 4.038A pdb=" N ALA D 660 " --> pdb=" O GLU D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 684 Processing helix chain 'D' and resid 687 through 699 removed outlier: 5.418A pdb=" N GLN D 697 " --> pdb=" O THR D 693 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 698 " --> pdb=" O ILE D 694 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS D 699 " --> pdb=" O ALA D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 720 removed outlier: 4.263A pdb=" N MET D 712 " --> pdb=" O LYS D 708 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET D 720 " --> pdb=" O MET D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 737 removed outlier: 4.368A pdb=" N ARG D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 19 removed outlier: 3.897A pdb=" N SER E 19 " --> pdb=" O LEU E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 71 Processing helix chain 'E' and resid 114 through 125 removed outlier: 3.926A pdb=" N ILE E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN E 123 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN E 124 " --> pdb=" O GLU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 239 removed outlier: 3.812A pdb=" N PHE E 227 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N SER E 237 " --> pdb=" O ARG E 233 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ARG E 238 " --> pdb=" O ALA E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 277 Processing helix chain 'E' and resid 286 through 291 removed outlier: 4.492A pdb=" N ILE E 290 " --> pdb=" O GLY E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 317 removed outlier: 4.364A pdb=" N ILE E 302 " --> pdb=" O SER E 298 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG E 303 " --> pdb=" O GLU E 299 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU E 305 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP E 308 " --> pdb=" O LYS E 304 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA E 309 " --> pdb=" O LEU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 334 removed outlier: 4.024A pdb=" N ILE E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 359 Processing helix chain 'E' and resid 375 through 378 removed outlier: 4.074A pdb=" N LEU E 378 " --> pdb=" O ARG E 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 375 through 378' Processing helix chain 'E' and resid 379 through 384 removed outlier: 3.671A pdb=" N LEU E 383 " --> pdb=" O ILE E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 411 Processing helix chain 'E' and resid 411 through 416 Processing helix chain 'E' and resid 425 through 433 removed outlier: 4.521A pdb=" N VAL E 431 " --> pdb=" O LYS E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 456 removed outlier: 3.889A pdb=" N ALA E 452 " --> pdb=" O ALA E 448 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N HIS E 456 " --> pdb=" O ALA E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 489 removed outlier: 3.940A pdb=" N SER E 483 " --> pdb=" O ASP E 479 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE E 488 " --> pdb=" O LEU E 484 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS E 489 " --> pdb=" O GLU E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 531 removed outlier: 3.954A pdb=" N THR E 515 " --> pdb=" O GLY E 511 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 561 removed outlier: 3.690A pdb=" N LEU E 552 " --> pdb=" O GLY E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 574 removed outlier: 3.649A pdb=" N ILE E 574 " --> pdb=" O ASP E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 584 Processing helix chain 'E' and resid 584 through 595 removed outlier: 3.926A pdb=" N ILE E 588 " --> pdb=" O ALA E 584 " (cutoff:3.500A) removed outlier: 4.262A 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: 4.834A pdb=" N LEU E 629 " --> pdb=" O ALA E 625 " (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: 3.780A pdb=" N GLN E 696 " --> pdb=" O THR E 692 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN E 697 " --> pdb=" O THR E 693 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS E 699 " --> pdb=" O ALA E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 719 removed outlier: 3.578A pdb=" N GLU E 715 " --> pdb=" O LEU E 711 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN E 719 " --> pdb=" O GLU E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 734 removed outlier: 4.179A pdb=" N ALA E 731 " --> pdb=" O ARG E 727 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 239 removed outlier: 3.570A pdb=" N PHE F 231 " --> pdb=" O PHE F 227 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG F 232 " --> pdb=" O SER F 228 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG F 233 " --> pdb=" O ASP F 229 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA F 234 " --> pdb=" O ILE F 230 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER F 237 " --> pdb=" O ARG F 233 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG F 238 " --> pdb=" O ALA F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 278 removed outlier: 3.588A pdb=" N GLY F 274 " --> pdb=" O ALA F 270 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN F 278 " --> pdb=" O GLY F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 316 removed outlier: 4.071A pdb=" N ARG F 303 " --> pdb=" O GLU F 299 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE F 306 " --> pdb=" O ILE F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 360 removed outlier: 4.483A pdb=" N ASN F 352 " --> pdb=" O ASP F 348 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE F 358 " --> pdb=" O LEU F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 411 Processing helix chain 'F' and resid 427 through 432 Processing helix chain 'F' and resid 443 through 448 Processing helix chain 'F' and resid 449 through 454 Processing helix chain 'F' and resid 498 through 503 removed outlier: 3.901A pdb=" N TYR F 502 " --> pdb=" O ASP F 498 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE F 503 " --> pdb=" O TYR F 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 498 through 503' Processing helix chain 'F' and resid 511 through 530 removed outlier: 3.639A pdb=" N THR F 515 " --> pdb=" O GLY F 511 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU F 524 " --> pdb=" O ASP F 520 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS F 529 " --> pdb=" O VAL F 525 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN F 530 " --> pdb=" O GLN F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 549 through 560 removed outlier: 3.527A pdb=" N SER F 560 " --> pdb=" O ILE F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 577 through 595 removed outlier: 3.555A pdb=" N GLN F 583 " --> pdb=" O THR F 579 " (cutoff:3.500A) removed outlier: 3.516A 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 631 removed outlier: 3.732A pdb=" N LEU F 623 " --> pdb=" O SER F 619 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS F 631 " --> pdb=" O LEU F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 656 Processing helix chain 'F' and resid 672 through 684 Processing helix chain 'F' and resid 687 through 696 removed outlier: 3.826A pdb=" N THR F 693 " --> pdb=" O LYS F 689 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE F 694 " --> pdb=" O GLU F 690 " (cutoff:3.500A) Processing helix chain 'F' and resid 706 through 720 removed outlier: 4.095A pdb=" N GLU F 715 " --> pdb=" O LEU F 711 " (cutoff:3.500A) removed outlier: 3.564A 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 21 through 35 removed outlier: 4.381A pdb=" N SER H 25 " --> pdb=" O LEU H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 83 removed outlier: 4.013A pdb=" N LYS H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU H 57 " --> pdb=" O GLN H 53 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP H 58 " --> pdb=" O GLY H 54 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS H 66 " --> pdb=" O GLU H 62 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU H 75 " --> pdb=" O MET H 71 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS H 76 " --> pdb=" O LYS H 72 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN H 77 " --> pdb=" O GLU H 73 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS H 79 " --> pdb=" O GLU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 202 removed outlier: 3.847A pdb=" N GLU H 148 " --> pdb=" O ASN H 144 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU H 151 " --> pdb=" O ASP H 147 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY H 158 " --> pdb=" O SER H 154 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN H 159 " --> pdb=" O GLY H 155 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN H 169 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU H 170 " --> pdb=" O ASP H 166 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE H 171 " --> pdb=" O MET H 167 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP H 172 " --> pdb=" O GLY H 168 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU H 183 " --> pdb=" O ASP H 179 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS H 184 " --> pdb=" O ARG H 180 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN H 188 " --> pdb=" O LYS H 184 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP H 193 " --> pdb=" O LYS H 189 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET H 202 " --> pdb=" O ARG H 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 237 removed outlier: 4.297A pdb=" N ILE I 202 " --> pdb=" O ARG I 198 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET I 221 " --> pdb=" O MET I 217 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU I 228 " --> pdb=" O GLU I 224 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N MET I 229 " --> pdb=" O SER I 225 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE I 230 " --> pdb=" O GLN I 226 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP I 231 " --> pdb=" O GLY I 227 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR I 235 " --> pdb=" O ASP I 231 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN I 236 " --> pdb=" O ARG I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 255 removed outlier: 3.904A pdb=" N ARG I 246 " --> pdb=" O ASP I 242 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP I 250 " --> pdb=" O ARG I 246 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS I 253 " --> pdb=" O SER I 249 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL I 255 " --> pdb=" O THR I 251 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 86 removed outlier: 3.646A pdb=" N VAL J 42 " --> pdb=" O GLN J 38 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU J 55 " --> pdb=" O ASP J 51 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN J 58 " --> pdb=" O LEU J 54 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG J 66 " --> pdb=" O GLU J 62 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP J 68 " --> pdb=" O ASP J 64 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA J 69 " --> pdb=" O ASP J 65 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA J 72 " --> pdb=" O ASP J 68 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY J 73 " --> pdb=" O ALA J 69 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG J 86 " --> pdb=" O ALA J 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 17 removed outlier: 3.878A pdb=" N LEU K 14 " --> pdb=" O ALA K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 54 removed outlier: 3.678A pdb=" N GLU K 43 " --> pdb=" O GLU K 39 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 77 removed outlier: 3.841A pdb=" N ASN K 63 " --> pdb=" O SER K 59 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN K 67 " --> pdb=" O ASN K 63 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA K 68 " --> pdb=" O ALA K 64 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU K 73 " --> pdb=" O ALA K 69 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN K 74 " --> pdb=" O GLN K 70 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU K 75 " --> pdb=" O LEU K 71 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLN K 76 " --> pdb=" O HIS K 72 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER K 77 " --> pdb=" O LEU K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 95 removed outlier: 4.085A pdb=" N PHE K 92 " --> pdb=" O ALA K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 113 removed outlier: 3.747A pdb=" N CYS K 103 " --> pdb=" O GLU K 99 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE K 108 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU K 109 " --> pdb=" O MET K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 134 removed outlier: 3.800A pdb=" N SER K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 154 removed outlier: 4.425A pdb=" N ALA K 143 " --> pdb=" O GLU K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 176 removed outlier: 3.972A pdb=" N TYR K 171 " --> pdb=" O LYS K 167 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN K 174 " --> pdb=" O GLY K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 195 removed outlier: 3.931A pdb=" N ASP K 194 " --> pdb=" O THR K 190 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER K 195 " --> pdb=" O SER K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 212 removed outlier: 4.362A pdb=" N ASP K 204 " --> pdb=" O TYR K 200 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS K 212 " --> pdb=" O LYS K 208 " (cutoff:3.500A) Processing helix chain 'K' and resid 219 through 228 Processing helix chain 'K' and resid 234 through 239 removed outlier: 3.786A pdb=" N ASP K 237 " --> pdb=" O ALA K 234 " (cutoff:3.500A) Processing helix chain 'K' and resid 241 through 253 removed outlier: 4.343A pdb=" N GLU K 249 " --> pdb=" O LYS K 245 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA K 250 " --> pdb=" O LYS K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 270 removed outlier: 3.808A pdb=" N THR K 260 " --> pdb=" O VAL K 256 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU K 261 " --> pdb=" O ASP K 257 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER K 262 " --> pdb=" O SER K 258 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL K 263 " --> pdb=" O TYR K 259 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU K 265 " --> pdb=" O GLU K 261 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER K 268 " --> pdb=" O LYS K 264 " (cutoff:3.500A) Processing helix chain 'K' and resid 273 through 292 Processing helix chain 'L' and resid 9 through 21 removed outlier: 3.693A pdb=" N LEU L 14 " --> pdb=" O ALA L 10 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA L 15 " --> pdb=" O MET L 11 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS L 20 " --> pdb=" O GLU L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 55 removed outlier: 4.152A pdb=" N GLU L 39 " --> pdb=" O SER L 35 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU L 40 " --> pdb=" O SER L 36 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN L 50 " --> pdb=" O ALA L 46 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS L 53 " --> pdb=" O ALA L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 74 removed outlier: 3.725A pdb=" N ALA L 69 " --> pdb=" O PHE L 65 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU L 71 " --> pdb=" O GLN L 67 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N HIS L 72 " --> pdb=" O ALA L 68 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN L 74 " --> pdb=" O GLN L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 95 removed outlier: 3.694A pdb=" N LYS L 94 " --> pdb=" O ASN L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 112 removed outlier: 3.662A pdb=" N CYS L 103 " --> pdb=" O GLU L 99 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE L 110 " --> pdb=" O ARG L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 134 removed outlier: 4.199A pdb=" N HIS L 123 " --> pdb=" O ILE L 119 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER L 126 " --> pdb=" O LYS L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 155 removed outlier: 3.565A pdb=" N GLN L 147 " --> pdb=" O ALA L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 171 removed outlier: 3.540A pdb=" N TYR L 171 " --> pdb=" O LYS L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 194 removed outlier: 3.546A pdb=" N ASP L 183 " --> pdb=" O GLN L 179 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU L 186 " --> pdb=" O ILE L 182 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLN L 187 " --> pdb=" O ASP L 183 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL L 188 " --> pdb=" O ILE L 184 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY L 189 " --> pdb=" O TYR L 185 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP L 194 " --> pdb=" O THR L 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 200 No H-bonds generated for 'chain 'L' and resid 198 through 200' Processing helix chain 'L' and resid 201 through 212 Processing helix chain 'L' and resid 219 through 228 removed outlier: 4.469A pdb=" N VAL L 225 " --> pdb=" O ALA L 221 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN L 226 " --> pdb=" O LYS L 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 252 removed outlier: 3.831A pdb=" N MET L 244 " --> pdb=" O GLU L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 256 through 268 removed outlier: 3.764A pdb=" N VAL L 263 " --> pdb=" O TYR L 259 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS L 264 " --> pdb=" O THR L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 273 through 292 removed outlier: 3.758A pdb=" N THR L 286 " --> pdb=" O ARG L 282 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE L 287 " --> pdb=" O ILE L 283 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN L 288 " --> pdb=" O LYS L 284 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP L 290 " --> pdb=" O THR L 286 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU L 292 " --> pdb=" O GLN L 288 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 282 through 285 removed outlier: 3.646A pdb=" N LYS A 283 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET A 372 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE A 256 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N THR A 373 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU A 258 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL A 391 " --> pdb=" O GLY A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 565 through 568 removed outlier: 6.371A pdb=" N LYS A 566 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 663 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 540 " --> pdb=" O THR A 663 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 10 removed outlier: 3.819A pdb=" N HIS B 34 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 81 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU B 79 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 135 through 140 removed outlier: 3.740A pdb=" N LEU B 148 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR B 96 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE B 152 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR B 94 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA B 154 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE B 92 " --> pdb=" O ALA B 154 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 111 through 113 removed outlier: 5.483A pdb=" N TYR B 112 " --> pdb=" O ILE B 196 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 129 through 131 Processing sheet with id=AA7, first strand: chain 'B' and resid 283 through 285 removed outlier: 6.596A pdb=" N ILE B 325 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N MET B 372 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE B 327 " --> pdb=" O MET B 372 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 373 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL B 391 " --> pdb=" O GLY B 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 565 through 568 removed outlier: 3.579A pdb=" N LYS B 566 " --> pdb=" O CYS B 599 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N SER B 598 " --> pdb=" O LEU B 641 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE B 643 " --> pdb=" O SER B 598 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 600 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N THR B 645 " --> pdb=" O VAL B 600 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B 602 " --> pdb=" O THR B 645 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 539 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N THR B 646 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU B 541 " --> pdb=" O THR B 646 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 670 through 672 removed outlier: 3.574A pdb=" N ALA B 671 " --> pdb=" O VAL B 703 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 10 removed outlier: 7.692A pdb=" N VAL C 60 " --> pdb=" O SER C 5 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLN C 7 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N PHE C 62 " --> pdb=" O GLN C 7 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ALA C 9 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N HIS C 43 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 81 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N SER C 40 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N GLU C 77 " --> pdb=" O SER C 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 135 through 140 removed outlier: 6.610A pdb=" N THR C 96 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE C 152 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR C 94 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA C 154 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE C 92 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLY C 93 " --> pdb=" O GLN C 182 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ALA C 184 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N MET C 95 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N GLU C 186 " --> pdb=" O MET C 95 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE C 97 " --> pdb=" O GLU C 186 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 111 through 113 removed outlier: 6.175A pdb=" N TYR C 112 " --> pdb=" O ILE C 196 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 131 Processing sheet with id=AB5, first strand: chain 'C' and resid 283 through 284 removed outlier: 6.917A pdb=" N LYS C 283 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N HIS C 323 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ILE C 370 " --> pdb=" O HIS C 323 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 325 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N MET C 372 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU C 258 " --> pdb=" O THR C 373 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 564 through 565 removed outlier: 6.661A pdb=" N PHE C 564 " --> pdb=" O CYS C 599 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N VAL C 601 " --> pdb=" O PHE C 564 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER C 598 " --> pdb=" O LEU C 641 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE C 643 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL C 600 " --> pdb=" O ILE C 643 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N THR C 645 " --> pdb=" O VAL C 600 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 4 through 10 removed outlier: 3.529A pdb=" N VAL D 24 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N HIS D 43 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N SER D 40 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 12.652A pdb=" N GLU D 77 " --> pdb=" O SER D 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 135 through 136 removed outlier: 4.091A pdb=" N ILE D 152 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN D 170 " --> pdb=" O ALA D 154 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 135 through 136 removed outlier: 6.800A pdb=" N THR D 96 " --> pdb=" O LYS D 150 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE D 152 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR D 94 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA D 154 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE D 92 " --> pdb=" O ALA D 154 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 112 through 113 removed outlier: 6.624A pdb=" N TYR D 112 " --> pdb=" O ILE D 196 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 129 through 131 Processing sheet with id=AC3, first strand: chain 'D' and resid 283 through 284 removed outlier: 6.975A pdb=" N LYS D 283 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU D 368 " --> pdb=" O HIS D 323 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR D 373 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 565 through 568 removed outlier: 6.539A pdb=" N SER D 598 " --> pdb=" O LEU D 641 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE D 643 " --> pdb=" O SER D 598 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL D 600 " --> pdb=" O ILE D 643 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N THR D 645 " --> pdb=" O VAL D 600 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL D 602 " --> pdb=" O THR D 645 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AC6, first strand: chain 'E' and resid 4 through 10 removed outlier: 8.022A pdb=" N VAL E 60 " --> pdb=" O SER E 5 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N GLN E 7 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N PHE E 62 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA E 9 " --> pdb=" O PHE E 62 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 135 through 136 Processing sheet with id=AC8, first strand: chain 'E' and resid 135 through 136 removed outlier: 6.585A pdb=" N THR E 96 " --> pdb=" O LYS E 150 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE E 152 " --> pdb=" O THR E 94 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR E 94 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ALA E 154 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE E 92 " --> pdb=" O ALA E 154 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLY E 93 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ALA E 184 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N MET E 95 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLU E 186 " --> pdb=" O MET E 95 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE E 97 " --> pdb=" O GLU E 186 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 112 through 113 removed outlier: 6.351A pdb=" N TYR E 112 " --> pdb=" O ILE E 196 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 128 through 131 Processing sheet with id=AD2, first strand: chain 'E' and resid 258 through 259 Processing sheet with id=AD3, first strand: chain 'E' and resid 283 through 285 removed outlier: 3.681A pdb=" N LYS E 283 " --> pdb=" O ILE E 324 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE E 325 " --> pdb=" O LEU E 368 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 540 through 542 removed outlier: 3.828A pdb=" N THR E 646 " --> pdb=" O LEU E 541 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS E 566 " --> pdb=" O CYS E 599 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP E 603 " --> pdb=" O CYS E 568 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 258 through 259 removed outlier: 7.023A pdb=" N LEU F 258 " --> pdb=" O THR F 373 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'F' and resid 283 through 286 removed outlier: 3.626A pdb=" N LEU F 368 " --> pdb=" O HIS F 323 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE F 325 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE F 370 " --> pdb=" O ILE F 325 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 564 through 568 removed outlier: 4.082A pdb=" N CYS F 599 " --> pdb=" O PHE F 564 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS F 566 " --> pdb=" O CYS F 599 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU F 641 " --> pdb=" O SER F 598 " (cutoff:3.500A) 1636 hydrogen bonds defined for protein. 4788 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: 27.97 Time building geometry restraints manager: 17.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 36434 1.01 - 1.22: 82 1.22 - 1.42: 14797 1.42 - 1.62: 21788 1.62 - 1.83: 358 Bond restraints: 73459 Sorted by residual: bond pdb=" C4 ATP B 802 " pdb=" N9 ATP B 802 " ideal model delta sigma weight residual 1.374 1.288 0.086 1.00e-02 1.00e+04 7.41e+01 bond pdb=" C5 ATP D 802 " pdb=" N7 ATP D 802 " ideal model delta sigma weight residual 1.387 1.313 0.074 1.00e-02 1.00e+04 5.42e+01 bond pdb=" C4 ATP B 801 " pdb=" N9 ATP B 801 " ideal model delta sigma weight residual 1.374 1.303 0.071 1.00e-02 1.00e+04 5.03e+01 bond pdb=" C4 ATP D 801 " pdb=" N9 ATP D 801 " ideal model delta sigma weight residual 1.374 1.304 0.070 1.00e-02 1.00e+04 4.89e+01 bond pdb=" C4 ATP C 801 " pdb=" N9 ATP C 801 " ideal model delta sigma weight residual 1.374 1.305 0.069 1.00e-02 1.00e+04 4.74e+01 ... (remaining 73454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.39: 132756 6.39 - 12.78: 422 12.78 - 19.17: 14 19.17 - 25.56: 29 25.56 - 31.94: 14 Bond angle restraints: 133235 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 136.83 107.81 29.02 1.00e+00 1.00e+00 8.42e+02 angle pdb=" PB ATP C 801 " pdb=" O3B ATP C 801 " pdb=" PG ATP C 801 " ideal model delta sigma weight residual 139.87 112.32 27.55 1.00e+00 1.00e+00 7.59e+02 angle pdb=" PB ATP F 801 " pdb=" O3B ATP F 801 " pdb=" PG ATP F 801 " ideal model delta sigma weight residual 139.87 112.50 27.37 1.00e+00 1.00e+00 7.49e+02 angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 113.20 26.67 1.00e+00 1.00e+00 7.12e+02 angle pdb=" PB ATP E 801 " pdb=" O3B ATP E 801 " pdb=" PG ATP E 801 " ideal model delta sigma weight residual 139.87 115.05 24.82 1.00e+00 1.00e+00 6.16e+02 ... (remaining 133230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 33582 35.92 - 71.84: 634 71.84 - 107.76: 29 107.76 - 143.68: 5 143.68 - 179.60: 2 Dihedral angle restraints: 34252 sinusoidal: 19323 harmonic: 14929 Sorted by residual: dihedral pdb=" CA PRO D 613 " pdb=" C PRO D 613 " pdb=" N ILE D 614 " pdb=" CA ILE D 614 " ideal model delta harmonic sigma weight residual 180.00 101.31 78.69 0 5.00e+00 4.00e-02 2.48e+02 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 -179.60 179.60 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA GLN B 496 " pdb=" C GLN B 496 " pdb=" N GLU B 497 " pdb=" CA GLU B 497 " ideal model delta harmonic sigma weight residual 180.00 122.10 57.90 0 5.00e+00 4.00e-02 1.34e+02 ... (remaining 34249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.596: 5643 0.596 - 1.191: 2 1.191 - 1.787: 3 1.787 - 2.382: 1 2.382 - 2.978: 2 Chirality restraints: 5651 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 0.39 -2.98 2.00e-01 2.50e+01 2.22e+02 chirality pdb=" CG LEU B 420 " pdb=" CB LEU B 420 " pdb=" CD1 LEU B 420 " pdb=" CD2 LEU B 420 " 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=" CG LEU B 682 " pdb=" CB LEU B 682 " pdb=" CD1 LEU B 682 " pdb=" CD2 LEU B 682 " both_signs ideal model delta sigma weight residual False -2.59 -0.65 -1.93 2.00e-01 2.50e+01 9.36e+01 ... (remaining 5648 not shown) Planarity restraints: 10852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA F 279 " -0.031 2.00e-02 2.50e+03 6.59e-02 4.34e+01 pdb=" C ALA F 279 " 0.114 2.00e-02 2.50e+03 pdb=" O ALA F 279 " -0.045 2.00e-02 2.50e+03 pdb=" N ARG F 280 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 199 " -0.029 2.00e-02 2.50e+03 6.38e-02 4.07e+01 pdb=" C ALA C 199 " 0.110 2.00e-02 2.50e+03 pdb=" O ALA C 199 " -0.044 2.00e-02 2.50e+03 pdb=" N LYS C 200 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 480 " -0.027 2.00e-02 2.50e+03 5.43e-02 2.95e+01 pdb=" C PHE B 480 " 0.094 2.00e-02 2.50e+03 pdb=" O PHE B 480 " -0.035 2.00e-02 2.50e+03 pdb=" N LEU B 481 " -0.032 2.00e-02 2.50e+03 ... (remaining 10849 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.90: 324 1.90 - 2.58: 83912 2.58 - 3.25: 221505 3.25 - 3.93: 272214 3.93 - 4.60: 430598 Nonbonded interactions: 1008553 Sorted by model distance: nonbonded pdb=" ND2 ASN E 435 " pdb="HD21 ASN E 495 " model vdw 1.231 2.600 nonbonded pdb=" HG2 ARG F 315 " pdb="HD11 LEU F 316 " model vdw 1.447 2.440 nonbonded pdb=" HG2 ARG F 315 " pdb="HD12 LEU F 316 " model vdw 1.466 2.440 nonbonded pdb=" CG ASN E 435 " pdb="HD21 ASN E 495 " model vdw 1.548 2.750 nonbonded pdb="HD22 ASN E 435 " pdb="HD21 ASN E 495 " model vdw 1.580 2.100 ... (remaining 1008548 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 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 373 o \ r resid 398 through 414 or resid 422 through 457 or resid 477 through 738 or res \ id 801)) selection = (chain 'F' and (resid 219 through 263 or (resid 264 and (name N or name CA or na \ me 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 322 or (resid 323 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 32 \ 4 through 457 or resid 477 through 738 or resid 801)) } ncs_group { reference = (chain 'B' and (resid 1 through 9 or (resid 10 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 resid 11 through \ 72 or (resid 73 and (name N or name CA or name C or name O or name CB or name O \ G or name H or name HA or name HB2 or name HB3)) or resid 74 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB or name HA or name HB \ 1 or name HB2 or name HB3)) or resid 89 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 \ or resid 215 through 240 or resid 250 through 457 or resid 459 through 547 or (r \ esid 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 'C' 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 H or name HA or name HB2 or name HB3)) \ or resid 74 through 87 or (resid 88 and (name N or name CA or name C or name O o \ r name CB or name HA or name HB1 or name HB2 or name HB3)) or resid 89 through 2 \ 01 or resid 215 through 240 or resid 250 through 457 or resid 470 or resid 472 o \ r (resid 475 and (name N or name CA or name C or name O or name CB or name CG1 o \ r name CG2 or name HA or name HB or name HG11 or name HG12 or name HG13 or name \ HG21 or name HG22 or name HG23)) or resid 476 through 547 or (resid 548 and (nam \ e N or name CA or name C or name O or name HA2 or name HA3)) or resid 549 throug \ h 738 or resid 801)) selection = (chain 'D' and (resid 1 through 9 or (resid 10 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 resid 11 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 HB \ 3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or nam \ e HZ1 or name HZ3)) or resid 201 or resid 215 through 240 or resid 250 through 4 \ 57 or resid 470 or resid 472 or (resid 475 and (name N or name CA or name C or n \ ame O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or n \ ame HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 476 thro \ ugh 738 or resid 801)) selection = (chain 'E' and (resid 1 through 9 or (resid 10 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 resid 11 through \ 72 or (resid 73 and (name N or name CA or name C or name O or name CB or name O \ G or name H or name HA or name HB2 or name HB3)) or resid 74 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB or name HA or name HB \ 1 or name HB2 or name HB3)) or resid 89 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 o \ r name HA or name HB or name HG21 or name HG22 or name HG23)) or resid 215 throu \ gh 457 or resid 470 or resid 472 or (resid 475 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 \ or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 476 \ 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)) } ncs_group { reference = chain 'K' selection = (chain 'L' and (resid 8 through 115 or (resid 116 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 HH21 or name HH22)) or resid 117 thr \ ough 158 or (resid 159 and (name N or name CA or name C or name O or name CB or \ name OG or name H or name HA or name HB2 or name HB3)) or resid 160 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 resid 223 through 293)) } 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.970 Extract box with map and model: 2.030 Check model and map are aligned: 0.400 Set scattering table: 0.500 Process input model: 120.090 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.240 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: 0.020 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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 : 0.016 0.152 36963 Z= 1.033 Angle : 1.673 29.023 49842 Z= 1.011 Chirality : 0.116 2.978 5651 Planarity : 0.009 0.076 6415 Dihedral : 12.419 179.603 14281 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.82 % Favored : 96.94 % Rotamer: Outliers : 0.38 % Allowed : 4.89 % Favored : 94.72 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.90 % Twisted General : 0.41 % 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: -3.67 (0.10), residues: 4570 helix: -2.68 (0.09), residues: 2040 sheet: -2.06 (0.16), residues: 622 loop : -2.06 (0.12), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.005 TRP B 510 HIS 0.027 0.005 HIS K 213 PHE 0.066 0.007 PHE A 589 TYR 0.060 0.006 TYR F 593 ARG 0.026 0.003 ARG B 691 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 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 THR 201 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 MET 14 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 292 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 277 time to evaluate : 4.424 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: A 724 TYR cc_start: 0.7384 (m-80) cc_final: 0.7170 (m-80) REVERT: C 155 MET cc_start: 0.7702 (mtm) cc_final: 0.7311 (mpp) REVERT: D 273 ILE cc_start: 0.9369 (mt) cc_final: 0.9149 (tp) REVERT: D 573 MET cc_start: 0.6589 (ptp) cc_final: 0.6349 (ptt) REVERT: F 354 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6324 (mt) REVERT: I 219 MET cc_start: 0.9354 (tmt) cc_final: 0.9055 (tpp) outliers start: 15 outliers final: 7 residues processed: 291 average time/residue: 1.1327 time to fit residues: 522.9521 Evaluate side-chains 225 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 217 time to evaluate : 4.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 385 optimal weight: 0.9990 chunk 346 optimal weight: 9.9990 chunk 192 optimal weight: 8.9990 chunk 118 optimal weight: 0.8980 chunk 233 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 358 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 217 optimal weight: 5.9990 chunk 266 optimal weight: 40.0000 chunk 415 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 ASN A 374 ASN A 669 ASN ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN B 696 GLN C 124 GLN C 272 GLN C 374 ASN C 435 ASN C 449 GLN ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 GLN D 449 GLN D 669 ASN D 697 GLN D 719 GLN ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 ASN E 696 GLN E 719 GLN F 675 GLN H 188 ASN H 196 ASN I 213 HIS K 123 HIS ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 ASN L 254 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 36963 Z= 0.230 Angle : 0.739 11.210 49842 Z= 0.396 Chirality : 0.063 1.675 5651 Planarity : 0.005 0.060 6415 Dihedral : 11.265 178.414 5242 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.29 % Favored : 95.65 % Rotamer: Outliers : 0.08 % Allowed : 1.59 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.95 (0.11), residues: 4570 helix: -1.92 (0.09), residues: 2098 sheet: -1.62 (0.17), residues: 624 loop : -1.92 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 510 HIS 0.008 0.001 HIS E 323 PHE 0.027 0.002 PHE A 589 TYR 0.032 0.002 TYR F 593 ARG 0.010 0.001 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 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 THR 201 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 MET 14 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 265 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 262 time to evaluate : 5.370 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 495 ASN cc_start: 0.6531 (t0) cc_final: 0.5818 (m-40) REVERT: D 589 PHE cc_start: 0.6892 (m-10) cc_final: 0.6198 (m-10) REVERT: L 23 ASN cc_start: 0.8973 (m-40) cc_final: 0.8773 (m-40) outliers start: 3 outliers final: 2 residues processed: 265 average time/residue: 1.1008 time to fit residues: 462.0252 Evaluate side-chains 226 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 224 time to evaluate : 4.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 230 optimal weight: 0.8980 chunk 128 optimal weight: 50.0000 chunk 345 optimal weight: 0.7980 chunk 282 optimal weight: 10.0000 chunk 114 optimal weight: 0.8980 chunk 415 optimal weight: 20.0000 chunk 449 optimal weight: 10.0000 chunk 370 optimal weight: 9.9990 chunk 412 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 chunk 333 optimal weight: 0.4980 overall best weight: 2.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 366 ASN A 669 ASN ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 ASN E 685 ASN ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN H 196 ASN ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36963 Z= 0.186 Angle : 0.621 10.990 49842 Z= 0.333 Chirality : 0.062 1.684 5651 Planarity : 0.004 0.065 6415 Dihedral : 10.318 177.103 5242 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.16 % Favored : 94.77 % Rotamer: Outliers : 0.05 % Allowed : 1.92 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.23 (0.11), residues: 4570 helix: -1.25 (0.10), residues: 2142 sheet: -1.25 (0.18), residues: 599 loop : -1.64 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 704 HIS 0.005 0.001 HIS C 410 PHE 0.020 0.001 PHE L 207 TYR 0.016 0.001 TYR F 593 ARG 0.006 0.001 ARG D 725 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 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 THR 201 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 MET 14 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 246 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 244 time to evaluate : 4.511 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: D 495 ASN cc_start: 0.6160 (t0) cc_final: 0.5866 (m-40) REVERT: D 589 PHE cc_start: 0.6654 (m-10) cc_final: 0.6159 (m-10) REVERT: E 1 MET cc_start: 0.8825 (ttt) cc_final: 0.8468 (tmm) REVERT: F 311 GLU cc_start: 0.9572 (tt0) cc_final: 0.9336 (tp30) REVERT: K 51 MET cc_start: 0.5524 (ppp) cc_final: 0.5219 (ppp) REVERT: L 23 ASN cc_start: 0.9005 (m-40) cc_final: 0.8777 (m-40) outliers start: 2 outliers final: 0 residues processed: 246 average time/residue: 1.0319 time to fit residues: 409.6732 Evaluate side-chains 225 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 5.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 410 optimal weight: 20.0000 chunk 312 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 198 optimal weight: 40.0000 chunk 279 optimal weight: 30.0000 chunk 417 optimal weight: 20.0000 chunk 441 optimal weight: 20.0000 chunk 217 optimal weight: 9.9990 chunk 395 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN A 669 ASN ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 ASN ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN H 196 ASN ** I 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 236 ASN ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36963 Z= 0.293 Angle : 0.658 10.748 49842 Z= 0.362 Chirality : 0.061 1.694 5651 Planarity : 0.005 0.087 6415 Dihedral : 10.270 175.731 5242 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.47 % Favored : 94.49 % Rotamer: Outliers : 0.03 % Allowed : 1.90 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.10 (0.11), residues: 4570 helix: -1.00 (0.10), residues: 2160 sheet: -1.36 (0.18), residues: 631 loop : -1.71 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 213 HIS 0.007 0.001 HIS F 666 PHE 0.018 0.002 PHE F 492 TYR 0.016 0.002 TYR D 724 ARG 0.006 0.001 ARG D 725 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 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 THR 201 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 MET 14 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 238 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 4.501 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: D 495 ASN cc_start: 0.6322 (t0) cc_final: 0.5677 (m-40) REVERT: E 1 MET cc_start: 0.8749 (ttt) cc_final: 0.8457 (tmm) REVERT: E 117 MET cc_start: 0.8100 (mmm) cc_final: 0.7628 (mmm) REVERT: F 311 GLU cc_start: 0.9571 (tt0) cc_final: 0.9343 (tp30) REVERT: I 219 MET cc_start: 0.9079 (tmm) cc_final: 0.8788 (mmm) REVERT: L 23 ASN cc_start: 0.9101 (m-40) cc_final: 0.8898 (m-40) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.9959 time to fit residues: 383.5646 Evaluate side-chains 218 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 4.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 367 optimal weight: 10.0000 chunk 250 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 328 optimal weight: 0.9990 chunk 182 optimal weight: 0.0040 chunk 376 optimal weight: 30.0000 chunk 305 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 225 optimal weight: 20.0000 chunk 396 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 overall best weight: 5.6002 ------------------------------------------------------------------------------- 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 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 ASN ** E 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN H 196 ASN ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 36963 Z= 0.221 Angle : 0.593 10.914 49842 Z= 0.320 Chirality : 0.061 1.710 5651 Planarity : 0.004 0.076 6415 Dihedral : 9.963 178.559 5242 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.11 % Favored : 93.87 % Rotamer: Outliers : 0.03 % Allowed : 1.36 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.86 (0.11), residues: 4570 helix: -0.74 (0.10), residues: 2177 sheet: -1.28 (0.18), residues: 644 loop : -1.66 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 213 HIS 0.005 0.001 HIS E 323 PHE 0.022 0.002 PHE D 589 TYR 0.012 0.001 TYR C 611 ARG 0.006 0.001 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 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 THR 201 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 MET 14 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 234 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 233 time to evaluate : 4.545 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: A 573 MET cc_start: 0.6107 (ptp) cc_final: 0.5853 (ptt) REVERT: D 453 MET cc_start: 0.8192 (ptm) cc_final: 0.7909 (ttt) REVERT: D 495 ASN cc_start: 0.6596 (t0) cc_final: 0.5778 (m-40) REVERT: E 1 MET cc_start: 0.8807 (ttt) cc_final: 0.7825 (mpp) REVERT: E 117 MET cc_start: 0.7839 (mmm) cc_final: 0.7372 (mmm) REVERT: F 372 MET cc_start: 0.1063 (ptt) cc_final: 0.0844 (ptt) REVERT: I 219 MET cc_start: 0.9142 (tmm) cc_final: 0.8832 (mmm) outliers start: 1 outliers final: 0 residues processed: 234 average time/residue: 0.9747 time to fit residues: 369.9297 Evaluate side-chains 216 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 4.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 148 optimal weight: 10.0000 chunk 397 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 259 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 442 optimal weight: 20.0000 chunk 367 optimal weight: 0.9980 chunk 204 optimal weight: 50.0000 chunk 36 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 ASN ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN H 196 ASN J 33 GLN ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 36963 Z= 0.235 Angle : 0.592 10.951 49842 Z= 0.322 Chirality : 0.061 1.719 5651 Planarity : 0.004 0.066 6415 Dihedral : 9.873 177.521 5242 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.41 % Favored : 93.57 % Rotamer: Outliers : 0.03 % Allowed : 1.31 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.12), residues: 4570 helix: -0.61 (0.10), residues: 2173 sheet: -1.34 (0.18), residues: 644 loop : -1.61 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 213 HIS 0.005 0.001 HIS E 252 PHE 0.022 0.002 PHE C 436 TYR 0.012 0.002 TYR C 611 ARG 0.015 0.001 ARG C 315 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 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 THR 201 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 MET 14 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 4.542 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: A 573 MET cc_start: 0.6459 (ptp) cc_final: 0.6118 (ptt) REVERT: E 1 MET cc_start: 0.8845 (ttt) cc_final: 0.7940 (mpp) REVERT: E 117 MET cc_start: 0.7785 (mmm) cc_final: 0.7299 (mmm) REVERT: F 372 MET cc_start: 0.1330 (ptt) cc_final: 0.1080 (ptt) REVERT: F 655 MET cc_start: 0.6032 (tpt) cc_final: 0.5328 (tpt) REVERT: I 219 MET cc_start: 0.9155 (tmm) cc_final: 0.8885 (mmm) outliers start: 1 outliers final: 0 residues processed: 226 average time/residue: 0.9613 time to fit residues: 349.6416 Evaluate side-chains 208 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 4.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 426 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 chunk 322 optimal weight: 6.9990 chunk 250 optimal weight: 7.9990 chunk 372 optimal weight: 7.9990 chunk 246 optimal weight: 2.9990 chunk 440 optimal weight: 3.9990 chunk 275 optimal weight: 50.0000 chunk 268 optimal weight: 20.0000 chunk 203 optimal weight: 50.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 ASN D 675 GLN ** E 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 ASN F 286 ASN ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN H 196 ASN ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36963 Z= 0.223 Angle : 0.587 10.956 49842 Z= 0.318 Chirality : 0.061 1.710 5651 Planarity : 0.004 0.049 6415 Dihedral : 9.764 176.431 5242 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.41 % Favored : 93.57 % Rotamer: Outliers : 0.03 % Allowed : 0.85 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.63 (0.12), residues: 4570 helix: -0.50 (0.11), residues: 2182 sheet: -1.34 (0.18), residues: 644 loop : -1.56 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 213 HIS 0.005 0.001 HIS D 323 PHE 0.017 0.002 PHE E 235 TYR 0.027 0.002 TYR L 200 ARG 0.012 0.001 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 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 THR 201 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 MET 14 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 218 time to evaluate : 4.505 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: A 573 MET cc_start: 0.6322 (ptp) cc_final: 0.6016 (ptt) REVERT: D 155 MET cc_start: 0.7489 (pmm) cc_final: 0.7210 (pmm) REVERT: D 495 ASN cc_start: 0.6474 (t0) cc_final: 0.5960 (m-40) REVERT: E 117 MET cc_start: 0.7713 (mmm) cc_final: 0.7243 (mmm) REVERT: F 372 MET cc_start: 0.1661 (ptt) cc_final: 0.1208 (ptt) outliers start: 1 outliers final: 0 residues processed: 219 average time/residue: 0.9791 time to fit residues: 345.6291 Evaluate side-chains 208 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 4.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 272 optimal weight: 0.9990 chunk 175 optimal weight: 5.9990 chunk 263 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 86 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 280 optimal weight: 0.9980 chunk 300 optimal weight: 5.9990 chunk 217 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 346 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 669 ASN ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 ASN E 685 ASN ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 159 ASN H 188 ASN H 196 ASN ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 36963 Z= 0.157 Angle : 0.551 11.205 49842 Z= 0.291 Chirality : 0.062 1.725 5651 Planarity : 0.004 0.049 6415 Dihedral : 9.515 176.038 5242 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.73 % Favored : 94.25 % Rotamer: Outliers : 0.03 % Allowed : 0.79 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.27 (0.12), residues: 4570 helix: -0.20 (0.11), residues: 2197 sheet: -1.13 (0.19), residues: 638 loop : -1.40 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 275 HIS 0.004 0.001 HIS C 410 PHE 0.015 0.001 PHE C 327 TYR 0.010 0.001 TYR B 593 ARG 0.006 0.000 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 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 THR 201 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 MET 14 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 4.502 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: A 573 MET cc_start: 0.6238 (ptp) cc_final: 0.5928 (ptt) REVERT: D 155 MET cc_start: 0.7514 (pmm) cc_final: 0.7266 (pmm) REVERT: D 495 ASN cc_start: 0.6366 (t0) cc_final: 0.5546 (m-40) REVERT: E 117 MET cc_start: 0.7689 (mmm) cc_final: 0.7214 (mmm) REVERT: F 372 MET cc_start: 0.1469 (ptt) cc_final: 0.1170 (ptt) REVERT: F 655 MET cc_start: 0.6122 (tpt) cc_final: 0.5786 (tpt) REVERT: I 219 MET cc_start: 0.9062 (tmm) cc_final: 0.8668 (mmm) outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 0.9562 time to fit residues: 341.3781 Evaluate side-chains 210 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 4.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 400 optimal weight: 20.0000 chunk 421 optimal weight: 20.0000 chunk 385 optimal weight: 4.9990 chunk 410 optimal weight: 20.0000 chunk 247 optimal weight: 0.8980 chunk 178 optimal weight: 6.9990 chunk 322 optimal weight: 10.0000 chunk 125 optimal weight: 50.0000 chunk 370 optimal weight: 5.9990 chunk 388 optimal weight: 5.9990 chunk 409 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 ASN ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 36963 Z= 0.212 Angle : 0.565 10.913 49842 Z= 0.305 Chirality : 0.061 1.714 5651 Planarity : 0.004 0.048 6415 Dihedral : 9.502 176.779 5242 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.52 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.23 (0.12), residues: 4570 helix: -0.16 (0.11), residues: 2190 sheet: -1.13 (0.19), residues: 642 loop : -1.39 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 213 HIS 0.004 0.001 HIS D 666 PHE 0.014 0.001 PHE E 235 TYR 0.032 0.001 TYR F 593 ARG 0.006 0.000 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 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 THR 201 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 MET 14 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 4.544 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 340 MET cc_start: 0.8216 (pmm) cc_final: 0.7624 (pmm) REVERT: A 573 MET cc_start: 0.6451 (ptp) cc_final: 0.6102 (ptt) REVERT: D 155 MET cc_start: 0.7547 (pmm) cc_final: 0.7299 (pmm) REVERT: D 495 ASN cc_start: 0.6728 (t0) cc_final: 0.5768 (m-40) REVERT: D 657 MET cc_start: 0.7298 (ppp) cc_final: 0.6870 (tmm) REVERT: E 1 MET cc_start: 0.8846 (ttt) cc_final: 0.8017 (mpp) REVERT: E 117 MET cc_start: 0.7667 (mmm) cc_final: 0.7184 (mmm) REVERT: F 372 MET cc_start: 0.1720 (ptt) cc_final: 0.1364 (ptt) REVERT: H 163 MET cc_start: 0.9274 (ptp) cc_final: 0.9071 (ptp) REVERT: H 167 MET cc_start: 0.9240 (tmm) cc_final: 0.8989 (tmm) REVERT: I 219 MET cc_start: 0.9075 (tmm) cc_final: 0.8647 (mmm) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 1.0296 time to fit residues: 358.1092 Evaluate side-chains 204 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 4.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 269 optimal weight: 40.0000 chunk 434 optimal weight: 7.9990 chunk 264 optimal weight: 20.0000 chunk 205 optimal weight: 30.0000 chunk 301 optimal weight: 3.9990 chunk 455 optimal weight: 20.0000 chunk 419 optimal weight: 10.0000 chunk 362 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 280 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN H 196 ASN ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36963 Z= 0.213 Angle : 0.571 11.038 49842 Z= 0.308 Chirality : 0.061 1.737 5651 Planarity : 0.004 0.050 6415 Dihedral : 9.499 175.838 5242 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.05 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.25 (0.12), residues: 4570 helix: -0.16 (0.11), residues: 2195 sheet: -1.15 (0.19), residues: 643 loop : -1.41 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 213 HIS 0.005 0.001 HIS D 323 PHE 0.016 0.002 PHE K 52 TYR 0.023 0.001 TYR F 593 ARG 0.006 0.001 ARG H 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9140 Ramachandran restraints generated. 4570 Oldfield, 0 Emsley, 4570 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 THR 201 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 MET 14 is missing expected H atoms. Skipping. Residue LYS 83 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 222 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 4.602 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 340 MET cc_start: 0.8237 (pmm) cc_final: 0.7718 (pmm) REVERT: A 573 MET cc_start: 0.6593 (ptp) cc_final: 0.6259 (ptt) REVERT: D 155 MET cc_start: 0.7589 (pmm) cc_final: 0.7344 (pmm) REVERT: E 117 MET cc_start: 0.7619 (mmm) cc_final: 0.7117 (mmm) REVERT: F 655 MET cc_start: 0.6480 (tpt) cc_final: 0.6227 (tpt) REVERT: I 219 MET cc_start: 0.9099 (tmm) cc_final: 0.8765 (mmm) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.9830 time to fit residues: 338.7941 Evaluate side-chains 204 residues out of total 3943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 4.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 457 random chunks: chunk 287 optimal weight: 20.0000 chunk 386 optimal weight: 20.0000 chunk 111 optimal weight: 1.9990 chunk 334 optimal weight: 6.9990 chunk 53 optimal weight: 30.0000 chunk 100 optimal weight: 4.9990 chunk 363 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 chunk 372 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 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 352 ASN ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 ASN ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN H 196 ASN ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.034495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.021136 restraints weight = 1279764.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.022095 restraints weight = 723860.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.023377 restraints weight = 423122.891| |-----------------------------------------------------------------------------| r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 36963 Z= 0.233 Angle : 0.579 10.954 49842 Z= 0.314 Chirality : 0.061 1.729 5651 Planarity : 0.004 0.050 6415 Dihedral : 9.514 175.947 5242 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.13 % Favored : 92.84 % 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 : 0.07 % 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: -1.33 (0.12), residues: 4570 helix: -0.25 (0.11), residues: 2205 sheet: -1.20 (0.19), residues: 636 loop : -1.42 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 213 HIS 0.006 0.001 HIS D 323 PHE 0.016 0.002 PHE A 215 TYR 0.022 0.002 TYR F 593 ARG 0.006 0.001 ARG H 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9594.58 seconds wall clock time: 166 minutes 58.40 seconds (10018.40 seconds total)